Miracle-dz/UniFAR-FTUs huggingface dataset:
Blocked edges on Eulerian maps and mobiles: application to spanning trees, hard particles and the Ising model

We introduce Eulerian maps with blocked edges as a general way to implement statistical matter models on random maps by a modification of intrinsic distances. We show how to code these dressed maps by means of mobiles, i.e. decorated trees with labelled vertices, leading to a closed system of recursion relations for their generating functions. We discuss particular solvable cases in detail, as well as various applications of our method to several statistical systems such as spanning trees on quadrangulations, mutually excluding particles on Eulerian triangulations or the Ising model on quadrangulations.
New promising Euphorbiaceae extracts with activity in human lymphocytes from primary cell cultures

Context: Euphorbiaceae plants exhibit anti-inflammatory and immunomodulatory properties. Methods: We evaluated the activity of 14 extracts from seven Euphorbiaceae plants on primary immune cell cultures from healthy individuals. Peripheral blood mononuclear cells (PBMC) were exposed to the extracts w/o phytohaemagglutinin A or cycloheximide as agents that induce proliferation or apoptosis in PBMC, respectively. Results: We found that five up to 14 Euphorbiaceae’s extracts had the ability to modulate at least one of the immune parameters evaluated in this study. However, only the latex extracts of Euphorbia cotinifolia and Euphorbia tirucalli strongly induced both proliferation and apoptosis in PBMC. These extracts were further subfractioned by silica gel column chromatography. Two subfractions with enhanced activity in comparison to the crude extracts were obtained. Although these subfractions induced proliferation on both CD3+ and CD3− cells, the most prominent effects were observed in the former subpopulation. Interestingly, the subfraction from E. tirucalli induced lymphocyte proliferation without the need of accessory cells; this ability was not inhibited by the carbohydrates d-galactose and α-Methyl-d-Mannopyranoside. Conclusions: Altogether, these results reveal the presence of novel candidates within the Euphorbia plants to induce proliferation and apoptosis in human lymphocytes, mainly in CD3+ T cells.
Hard‐coding bottom‐up code generation tables to save time and space

Code generators based on bottom‐up rewrite systems (BURS) are automatically generated from machine‐description grammars. They produce locally optimal code for expression trees, but their tables are large and require compile‐time interpretation. This paper describes a program that compiles BURS tables into a combination of hard code and data. Hard‐coding exposed important opportunities for compression that were previously hidden in the tables, so the hard‐coded code generators are not just faster but also significantly smaller than their predecessors. A VAX code generator takes 21.4Kbytes and identifies optimal assembly code in about 50 VAX instructions per node.
Evaluating the Effectiveness of a Special Needs Diversionary Program in Reducing Reoffending Among Mentally Ill Youthful Offenders

The goal of this study was to evaluate the effectiveness of a mental health intervention for youthful offenders, specifically the Special Needs Diversionary Program (SNDP) by comparing the treatment group with the control group. The sample consisted of 328 mentally ill youths: 168 youths participated in the SNDP and 160 youths in other court-ordered programs. To examine the empirical relationships among the covariates, the current study uses a two-step approach: (a) logistic regression; and (b) Cox Proportional-Hazards Regression. The findings reveal that participation in the SNDP was strongly associated with reduced recidivism compared with nonparticipation in the SNDP among mentally ill youthful offenders throughout the 12-month follow-up. Study limitations and implications for future research are discussed.
Decellularized ECM-Derived Hydrogels: Modification and Properties

Extracellular matrix (ECM) hydrogels are water-swollen fibrillary three-dimensional (3D) networks where collagen type I is the major component. The hierarchical network formed by the polymerization of tropocollagen molecules with enhanced properties is an attractive template for generating biomaterials. The mammalian tissue source from which collagen is extracted and its consequent modification are variables that impact the physicochemical and biological properties of the collagen network. This chapter has the purpose to provide a review of the research of different strategies to modify and characterize the properties of decellularized ECM-derived hydrogels in the context of safe biomaterials with immunomodulatory properties.
Toward the integration of Omics data in epidemiological studies: still a “long and winding road”

Primary and secondary prevention can highly benefit a personalized medicine approach through the accurate discrimination of individuals at high risk of developing a specific disease from those at moderate and low risk. To this end precise risk prediction models need to be built. This endeavor requires a precise characterization of the individual exposome, genome, and phenome. Massive molecular omics data representing the different layers of the biological processes of the host and the nonhost will enable to build more accurate risk prediction models. Epidemiologists aim to integrate omics data along with important information coming from other sources (questionnaires, candidate markers) that has been proved to be relevant in the discrimination risk assessment of complex diseases. However, the integrative models in large‐scale epidemiologic research are still in their infancy and they face numerous challenges, some of them at the analytical stage. So far, there are a small number of studies that have integrated more than two omics data sets, and the inclusion of non‐omics data in the same models is still missing in most of studies. In this contribution, we aim at approaching the omics and non‐omics data integration from the epidemiology scope by considering the “massive” inclusion of variables in the risk assessment and predictive models. We also provide already available examples of integrative contributions in the field, propose analytical strategies that allow considering both omics and non‐omics data in the models, and finally review the challenges imbedding this type of research.
Interferon beta in multiple sclerosis: experience in a British specialist multiple sclerosis centre

Background: The efficacy of interferon beta (IFN beta) is well established in relapsing-remitting multiple sclerosis (MS). However, the use of this drug in clinical practice is complex, especially because it is only partially effective, its long term efficacy and side effects are unknown, its efficacy may be abrogated by the development of neutralising antibodies, compliance is variable, and its cost effectiveness is controversial. Objectives and Methods: Analysis of a prospectively followed up series of 101 MS patients treated with IFN beta was undertaken to: (1) monitor the outcome of IFN beta treatment in clinical practice; (2) compare the immunogenicity of the three commercial IFN beta preparations available; (3) assess the proportion of patients fulfilling the current guidelines of the Association of British Neurologists for stopping IFN beta therapy. Results: During a median treatment period of 26 months (range 2–85), the relapse rate decreased by 41%. Although the reduction in the relapse rate was similar for all three commercial products, none of the Avonex treated patients were relapse free, compared with 19% of the Betaferon treated and 27% of the Rebif treated patients (p=0.02). Neutralising antibodies were not detected in Avonex treated patients (0 of 18), compared with 12 of 32 (38%) Betaferon treated and 10 of 23 (44%) Rebif treated patients (p=0.02). Forty of 101 (40%) patients satisfied the current (2001) Association of British Neurologists criteria for stopping IFN beta treatment at some stage during their treatment. Conclusion: IFN beta is effective in reducing the relapse rate in patients with relapsing-remitting MS in routine clinical practice. However, after a median treatment duration of 26 months, 40% of initially relapsing-remitting MS patients seem to have ongoing disease activity, presenting as disabling relapses or insidious progression.
Autodigestion: Proteolytic Degradation and Multiple Organ Failure in Shock

ABSTRACT There is currently no effective treatment for multiorgan failure following shock other than supportive care. A better understanding of the pathogenesis of these sequelae to shock is required. The intestine plays a central role in multiorgan failure. It was previously suggested that bacteria and their toxins are responsible for the organ failure seen in circulatory shock, but clinical trials in septic patients have not confirmed this hypothesis. Instead, we review here evidence that the digestive enzymes, synthesized in the pancreas and discharged into the small intestine as requirement for normal digestion, may play a role in multiorgan failure. These powerful enzymes are nonspecific, highly concentrated, and fully activated in the lumen of the intestine. During normal digestion they are compartmentalized in the lumen of the intestine by the mucosal epithelial barrier. However, if this barrier becomes permeable, e.g. in an ischemic state, the digestive enzymes escape into the wall of the intestine. They digest tissues in the mucosa and generate small molecular weight cytotoxic fragments such as unbound free fatty acids. Digestive enzymes may also escape into the systemic circulation and activate other degrading proteases. These proteases have the ability to clip the ectodomain of surface receptors and compromise their function, for example cleaving the insulin receptor causing insulin resistance. The combination of digestive enzymes and cytotoxic fragments leaking into the central circulation causes cell and organ dysfunction, and ultimately may lead to complete organ failure and death. We summarize current evidence suggesting that enteral blockade of digestive enzymes inside the lumen of the intestine may serve to reduce acute cell and organ damage and improve survival in experimental shock.
BERGMANN'S RULE AND VARIATION IN STRUCTURES RELATED TO FEEDING IN THE GRAY SQUIRREL

The general correlation of size with latitude in homeothermic animals was first noted by C. Bergmann (1847), who held that thermoregulatory factors, especially surface-volume ratio, operate to bring about size clines. Subsequent work on this subject has taken three approaches. First, Bergmann's claims have been subjected to increasingly detailed analysis and substantially redefined. Scholander (1955, 1956), Irving (1957), and Hayward (1965) disputed the notion that size differences confer actual functional advantages in thermoregulation, and claimed t~at insulation and behavior are the principal thermoregulatory devices. Mayr (1956, 1963) and Kendeigh (1969) defende.d Bergmann's observations, but Mayr redefined the rule by casting it in terms of size differences between races of a given species a.nd asserting that its validity ought not be tied to any particular physiological explanation. Rensch (1939), Hamilton (1958), and James (1970) found size clines to be best correlated with winter minimum temperature, aridity, and a combination of temperature and humidity, respectively. The present status of this path of research may be summarized by James's reformulation of the rule, called by her (p. 387) the "Neo-Bergmannian Rule" as follows:
On the benefits of the remote GPU virtualization mechanism: The rCUDA case

Graphics processing units (GPUs) are being adopted in many computing facilities given their extraordinary computing power, which makes it possible to accelerate many general purpose applications from different domains. However, GPUs also present several side effects, such as increased acquisition costs as well as larger space requirements. They also require more powerful energy supplies. Furthermore, GPUs still consume some amount of energy while idle, and their utilization is usually low for most workloads. In a similar way to virtual machines, the use of virtual GPUs may address the aforementioned concerns. In this regard, the remote GPU virtualization mechanism allows an application being executed in a node of the cluster to transparently use the GPUs installed at other nodes. Moreover, this technique allows to share the GPUs present in the computing facility among the applications being executed in the cluster. In this way, several applications being executed in different (or the same) cluster nodes can share 1 or more GPUs located in other nodes of the cluster. Sharing GPUs should increase overall GPU utilization, thus reducing the negative impact of the side effects mentioned before. Reducing the total amount of GPUs installed in the cluster may also be possible. In this paper, we explore some of the benefits that remote GPU virtualization brings to clusters. For instance, this mechanism allows an application to use all the GPUs present in the computing facility. Another benefit of this technique is that cluster throughput, measured as jobs completed per time unit, is noticeably increased when this technique is used. In this regard, cluster throughput can be doubled for some workloads. Furthermore, in addition to increase overall GPU utilization, total energy consumption can be reduced up to 40%. This may be key in the context of exascale computing facilities, which present an important energy constraint. Other benefits are related to the cloud computing domain, where a GPU can be easily shared among several virtual machines. Finally, GPU migration (and therefore server consolidation) is one more benefit of this novel technique.
Phylogenetics and the Human Microbiome

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
Comparative Short-term Benefits of Laparoscopic Liver Resection: 9000 Cases and Climbing

Objective:To perform a systematic review of worldwide literature on laparoscopic liver resections (LLR) and compare short-term outcomes against open liver resections (OLR) by meta-analyses. Summary Background Data:There are no updated pooled data since 2009 about the current status and short-term outcomes of LLR worldwide. Patients and Methods:All English language publications on LLR were screened. Descriptive worldwide data and short-term outcomes were obtained. Separate analyses were performed for minor-only and major-only resection series, and series in which minor/major resections were not differentiated. Apparent case duplications were excluded. Results:A set of 463 published manuscripts were reviewed. One hundred seventy-nine single-center series were identified that accounted for 9527 LLR cases worldwide. Minor-only, major-only, and combined major–minor series were 61, 18, and 100, respectively, including 32, 8, and 43 comparative series, respectively. Of the total 9527 LLR cases reported, 6190 (65%) were for malignancy and 3337 (35%) were for benign indications. There were 37 deaths reported (mortality rate = 0.4%). From the meta-analysis comparing case-matched LLR to OLR (N = 2900 cases), there was no increased mortality and significantly less complications, transfusions, blood loss, and hospital stay observed in LLR vs OLR. Conclusions:This is the largest review of LLR available to date with over 9000 cases published. It confirms growing safety when performed in selected patients and by trained surgeons, and suggests that LLR may offer improved patient short-term outcomes compared with OLR. Improved levels of evidence, standardized reporting of outcomes, and assuring proper training are the next challenges of laparoscopic liver surgery.
Imaging methodology and protocols for three-dimensional echocardiography

Purpose of review Three-dimensional echocardiography (3DE) is an additional ultrasound modality that is poised to become an integral part of the routine echocardiogram. Incorporating 3DE into clinical daily practice continues to be a challenge for many laboratories. The following review will focus on workflow processes related to methodology and protocols in order to incorporate 3DE into clinical practice. Recent findings Several studies have shown the clinical utility and feasibility of both transthoracic and transesophageal 3DE. In addition, many centers performing 3DE studies utilize a focused 3DE protocol as opposed to a full 3DE protocol. A majority of the studies noted limitations with respect to artifacts inherent in gated imaging and preferred real-time 3DE or rather volume imaging. A recurrent message from several recent publications is that the ultimate success and widespread clinical application of 3DE will rely mainly on improved 3D image resolution and volume rates. Summary Continuous technology improvements have led to real-time full-volume 3D imaging that is no longer prone to the artifact issues encountered with gated 3D imaging. Additional improvements to 3DE image quality and time-saving automatic quantitative analysis tools will continue to define the emerging role for routine 3DE.
Mental Health Workers’ Views on Addressing Tobacco Use

Objective: The aims of this study were to assess mental health workers’ attitudes to addressing tobacco dependence with patients, to identify barriers that may prevent people with mental illness from receiving support, and determine workers’ recommendations for tobacco policy and practice change. Method: Questionnaires were sent to government and non-government mental health services in Adelaide, South Australia. The questionnaires asked workers to rate on a Likert rating scale their attitudes to addressing tobacco use with patients and to respond to qualitative questions about managing tobacco use within mental health services. Quantitative data were analysed using SPSS version 15.0 and qualitative data was coded by three researchers into categories or themes and then analysed. Results: Questionnaires (324) were received from staff across 45 organizations providing clinical and psychosocial services. More than two thirds of the participants felt it was important for mental health services to be involved in assisting patients to quit smoking; however, only 26% said they raised the issue of tobacco use with patients, often or as part of the assessment. Respondents on average felt approximately one third of their patients could quit or reduce tobacco use if they received nicotine replacement therapy, information and support. Most workers suggested changes to policy and practice within mental health services including smoke free areas and the provision of information and support. Discussion: The rate of tobacco use amongst people with mental illness is still very high with serious social and health consequences. Mental health workers are uniquely placed to assist patients to quit or reduce tobacco use. This study has shown many workers believe that it is important to address tobacco use with their patients as part of routine care and that mental health services should implement significant tobacco policy and practice change.
Utility of 18F-FDG PET/CT uptake patterns in Waldeyer's ring for differentiating benign from malignant lesions in lateral pharyngeal recess of nasopharynx.

UNLABELLED Focally increased (18)F-FDG uptake in the lateral pharyngeal recess (LPR) of the nasopharynx due to a benign or malignant lesion is not an uncommon finding on PET images. The aim of this study was to evaluate whether, on PET/CT images, (18)F-FDG uptake occurs with characteristic patterns and intensities in various regions of Waldeyer's ring that can improve our ability to differentiate benign from malignant lesions. METHODS Data generated from the (18)F-FDG PET/CT images of 1,628 subjects in our cancer-screening program were analyzed. Increased uptake in the LPR was observed in 80 subjects (4.9%) presenting with benign lesions, including 53 subjects without and 27 subjects with symptoms of upper airway discomfort. In addition, 30 healthy controls and 21 patients with newly diagnosed nasopharyngeal carcinoma were recruited for this study. Visual uptake, measurements of the lesions' standardized uptake value (SUV), and any abnormalities on PET/CT were evaluated. The receiver-operating-characteristic curve and area under the curve were applied to evaluate the discriminating power. RESULTS Increased (18)F-FDG uptake (SUV, mean +/- SD) was found in the LPR, with a statistically significant (P < 0.001) difference between benign lesions (3.0 +/- 1.16) and malignant lesions (7.03 +/- 3.83). However, associated increased uptake exclusively in the palatine tonsil, lingual tonsil, and submandibular gland was found in both asymptomatic and symptomatic subjects. The ratio of LPR uptake to palatine tonsil uptake (N/P ratio) in benign lesions (0.81 +/- 0.37) was significantly (P < 0.001) lower than that in malignant lesions (2.30 +/- 1.62). Higher incidences of asymmetric (18)F-FDG LPR uptake, cervical lymph node uptake, and asymmetric wall thickening of the LPR on CT were observed in patients with nasopharyngeal carcinoma. When an SUV of less than 3.9 and an N/P ratio of less than 1.5 were used as cutoff points in subjects showing the combination of symmetric uptake in the LPR and normal or symmetric wall thickening, and detectable lymph node uptake, the area under the curve for benign lesions on PET/CT was 0.932 +/- 0.042 (95% confidence interval, 0.86-0.98), with a sensitivity of 90.4% and a specificity of 93.8%. CONCLUSION The intensity and patterns of (18)F-FDG uptake in various regions of Waldeyer's ring along with CT scan findings provide a feasible modality to differentiate benign from malignant nasopharyngeal lesions.
From Design to Earthquake Loss Assessment of Steel Moment-Resisting Frames

Steel moment-resisting frames (MRFs) are well known for their ductile and stable hysteretic behaviour. For this reason, they are an attractive and effective structural system for seismic resistance. Current seismic design codes, namely Eurocode 8, provide system performance factors that should be used in the seismic design under different ductility classes. However, recent research studies have shown that the use of the code-prescribed performance factors lead to stiffer and heavier structural solutions that are not consistent with the performance-based design assumptions. A new methodology, Improved Force-Based Design (IFBD), has recently been proposed with the aim of a more rational determination of the adopted value of the behaviour factor, q, instead of using the upper bound reference values provided by the design code. This paper investigates if the obtained values of q for both EC8 and IFBD concerning steel MRFs are not only adequate, but also provide sufficient margins against collapse under maximum considered earthquake (MCE) ground motions. To this end, the methodology proposed in FEMA P695 was used. Additionally, the expected direct economic seismic losses are computed according to the PEER-PBEE methodology.