Miracle-dz/UniFAR-FTUs huggingface dataset:
Universal Bounds on Coarsening Rates for Mean-Field Models of Phase Transitions

We prove one-sided universal bounds on coarsening rates for two kinds of mean-field models of phase transitions, one with a coarsening rate $l \sim t^{1/3}$ and the other with $l\sim t^{1/2}$. Here l is a characteristic length scale. These bounds are both proved by following a strategy developed by Kohn and Otto [ Comm. Math. Phys., 229 (2002), pp. 375--395]. The $l\sim t^{1/2}$ rate is proved using a new dissipation relation which extends the Kohn--Otto method. In both cases, the dissipation relations are subtle and their proofs are based on a residual lemma (Lagrange identity) for the Cauchy--Schwarz inequality.
Finding anchors for genomic sequence comparison

Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole genomes generally use a seed-and-extend technique, starting from exact or near-exact matches and selecting a reliable subset of these, called anchors, and then filling in the remaining portions between the anchors using a combination of local and global alignment algorithms, but their choices for the parameters so far have been primarily heuristic. We present a statistical framework and practical methods for selecting a set of matches that is both sensitive and specific and can constitute a reliable set of anchors for a one-to-one mapping of two genomes from which a whole-genome alignment can be built. Starting from exact matches, we introduce a novel per-base repeat annotation, the $Z$-score, from which noise and repeat filtering conditions are explored. Dynamic programming-based chaining algorithms are also evaluated as context-based filters. We apply the methods described here to the comparison of two progressive assemblies of the human genome, NCBI build 28 and build 34 http://genome.ucsc. edu), and show that a significant portion of the two genomes can be found in selected exact matches, with very limited amount of sequence duplication.
The Tumorigenicity of Multipotent Adult Germline Stem Cells Transplanted into the Heart Is Affected by Natural Killer Cells and by Cyclosporine A Independent of Its Immunosuppressive Effects

Transplantation of stem cells represents an upcoming therapy for many degenerative diseases. For clinical use, transplantation of pluripotent stem cell-derived cells should lead to integration of functional grafts without immune rejection or teratoma formation. Our previous studies showed that the risk of teratoma formation is highly influenced by the immune system of the recipients. In this study, we have observed a higher teratoma formation rate when undifferentiated so-called multipotent adult germline stem cells (maGSCs) were transplanted into the heart of T, B, and natural killer (NK) cell-deficient RAG2−/−γc−/− mice than in RAG2−/− mice, which still have NK cells. Notably, in both strains, the teratoma formation rate was significantly reduced by the immunosuppressive drug cyclosporine A (CsA). Thus, CsA had a profound effect on teratoma formation independent of its immunosuppressive effects. The transplantation into RAG2−/− mice led to an activation of NK cells, which reached the maximum 14 days after transplantation and was not affected by CsA. The in vivo-activated NK cells efficiently killed YAC-1 and also maGSC target cells. This NK cell activation was confirmed in C57BL/6 wild-type mice whether treated with CsA or not. Sham operations in wild-type mice indicated that the inflammatory response to open heart surgery rather than the transplantation of maGSCs activated the NK cell system. An activation of NK cells during the transplantation of stem cell-derived in vitro differentiated grafts might be clinically beneficial by reducing the risk of teratoma formation by residual pluripotent cells.
Kinetic parameters of bone marrow stem cells using in vivo suicide by tritiated thymidine or by hydroxyurea.

The kinetics of colony-forming units (CFU) of the bone marrow in mice were studied using a method involving the suicide of cells in vivo by 3H-TdR or hydroxyurea. After selectively killing cells in S phase, the surviving cells traversed S phase in a cyclic fashion. This enabled the duration of the cycle and of the S phase of CFU to be measured—8 hr and 4 hr, respectively. It was shown that quiescent stem cells pass into the proliferative compartment. A computer model helped to explain the experimental results. The feedback mechanism seemed to be initiated by the depletion of the compartment of maturing cells. This hypothesis is supported by the fact that the CFU response to S-phase cell killing was similar in two strains of mice and was independent of the proportion of CFU in S phase, which was approximately 0% in the C57BI and 20% in the C3H mice.
Designing A Generalized NF2 Model with an SQL-Type Language Interface

Because of its small set of data types, the rela-tional model is constrained to simply structured data management tasks. For more advanced applications like engineering databases in the CAD/CAN area even a powerful extension like the NF' model is insufficient , yet: Important concepts like order and duplicates are not supported appropriately, and the free usage of composite items is prohibited by inherent asymmetries. These drawbacks can be removed by a data model which suooorts atomic data, lists, multisets, and tUpleS in"an orthogonal fashion. The necessary operations can be provided in an SQL-like framework. Compared with existing approaches, the expressive power could considerably be increased; nevertheless, the proposed SQL dialect has not become more complicated for comparable tasks, but more consistent and easier to understand.
Is the Poly (L- Lactide- Co– Caprolactone) Nanofibrous Membrane Suitable for Urinary Bladder Regeneration?

The purpose of this study was to compare: a new five-layered poly (L–lactide–co–caprolactone) (PLC) membrane and small intestinal submucosa (SIS) as a control in rat urinary bladder wall regeneration. The five-layered poly (L–lactide–co–caprolactone) membrane was prepared by an electrospinning process. Adipose tissue was harvested from five 8-week old male Wistar rats. Adipose derived stem cells (ADSCs) were seeded in a density of 3×106 cells/cm2 onto PLC membrane and SIS scaffolds, and cultured for 5-7 days in the stem cell culture medium. Twenty male Wistar rats were randomly divided into five equal groups. Augmentation cystoplasty was performed in a previously created dome defect. Groups: (I) PLC+ 3×106ADSCs; (II) SIS+ 3×106ADSCs; (III) PLC; (IV) SIS; (V) control. Cystography was performed after three months. The reconstructed urinary bladders were evaluated in H&E and Masson's trichrome staining. Regeneration of all components of the normal urinary bladder wall was observed in bladders augmented with cell-seeded SIS matrices. The urinary bladders augmented with SIS matrices without cells showed fibrosis and graft contraction. Bladder augmentation with the PLC membrane led to numerous undesirable events including: bladder wall perforation, fistula or diverticula formation, and incorporation of the reconstructed wall into the bladder lumen. The new five-layered poly (L–lactide–co–caprolactone) membrane possesses poorer potential for regenerating the urinary bladder wall compared with SIS scaffold.
High-Fat Diet Alters K+-Currents in Porcine Coronary Arteries and Adenosine Sensitivity during Metabolic Inhibition

Abstract: Coronary arteries from animals on normal diets (ND) exhibit well-maintained responses to dilators under ischemic conditions. The reported altered metabolic requirements and K+-currents in blood vessels from hypercholesterolemic animals fed high-fat diets (HF) led us to hypothesize that under metabolically depressed conditions (N2/2-deoxyglucose) coronary arteries from pigs would exhibit significantly decreased responses to adenosine (ADO) as compared with pigs given ND. Diet had no major effect on responses of coronary rings to ET-1, nor on the sensitivity to ADO or 2-chloroadenosine (2-CAD) relaxation under metabolically supported conditions. During metabolic inhibition the response curves for both ADO and 2-CAD were shifted to the right (P < 0.05), with the HF group shifted about 4-fold more than ND (P < 0.05). To determine the involvement of K+-channels, ADO responses were measured in the presence of 4-aminopyridine (4-AP, 1 mM) or glybenclamide (GLYB, 10 μM). The larger shift in the HF group during metabolic inhibition was not affected by GLYB, but disappeared in the presence of 4-AP with ND now behaving similarly to HF. These results indicate that HF diet may have a 4-AP–like effect on voltage-dependent K+-channels (KV). Patch-clamp measures of whole cell K+- currents showed the HF cells to have reduced 4-AP sensitive currents (P < 0.02). The 4-AP insensitive currents were similar in both groups. Thus, reduced KV channel activity may play a role in the depressed ADO relaxation associated with metabolic inhibition of HF coronary arteries. These factors may place the coronary circulation of HF at increased risk during an ischemic episode.
Adherence With Antihypertensive Drug Therapy and the Risk of Heart Failure in Clinical Practice

Randomized clinical trials have shown that antihypertensive treatment reduces the risk of heart failure (HF). Limited evidence exists, however, on whether and to what extent this benefit is translated into real-life practice. A nested case–control study was carried out by including the cohort of 76 017 patients from Lombardy (Italy), aged 40 to 80 years, who were newly treated with antihypertensive drugs during 2005. Cases were the 622 patients who experienced hospitalization for HF from initial prescription until 2012. Up to 5 controls were randomly selected for each case. Logistic regression was used to model the HF risk associated with adherence to antihypertensive drugs, which was measured by the proportion of days covered by treatment (PDC). Data were adjusted for several covariates. Sensitivity analyses were performed to account for possible sources of systematic uncertainty. Compared with patients with very low adherence (PDC, ⩽25%), low, intermediate, and high adherences were associated with progressively lower risk of HF, reduction in the high-adherence group (>75%) being 34% (95% confidence interval, 17%–48%). Similar effects were observed in younger (40–70 years) and older (71–80 years) patients and between patients treated with angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and diuretics. There was no evidence that adherence with calcium-channel blockers reduced the HF risk. Antihypertensive treatment lowers the HF risk in real-life practice, but adherence to treatment is necessary for a substantial benefit to take place. This is the case with a variety of antihypertensive drugs.
Multi-affinity spectral clustering

Spectral clustering (SC) has become one of the most popular clustering methods. Given an affinity matrix, SC explores its spectral-graph structure to partition data into disjoint meaningful groups. However, in many applications, there are multiple potentially useful features and thereby multiple affinity matrices. For applying spectral clustering to such cases, these affinity matrices must be aggregated into a single one. Unfortunately, affinity measures based on different features could have different characteristics. Some are more effective than others. We propose a multi-affinity spectral clustering (MASC) algorithm which extends the SC algorithm with multiple affinities available. By automatically adjusting the weights of affinity matrices, MASC is more immune to ineffective affinities and irrelevant features. This makes the choice of similarity or distance-metric measures for clustering less crucial. Experiments show that MASC is effective in simultaneous clustering and feature fusion, thus maintaining robustness of SC for multi-affinity clustering problems.
Antiretroviral Therapy for HIV-2 Infection: Recommendations for Management in Low-Resource Settings

HIV-2 contributes approximately a third to the prevalence of HIV in West Africa and is present in significant amounts in several low-income countries outside of West Africa with historical ties to Portugal. It complicates HIV diagnosis, requiring more expensive and technically demanding testing algorithms. Natural polymorphisms and patterns in the development of resistance to antiretrovirals are reviewed, along with their implications for antiretroviral therapy. Nonnucleoside reverse transcriptase inhibitors, crucial in standard first-line regimens for HIV-1 in many low-income settings, have no effect on HIV-2. Nucleoside analogues alone are not sufficiently potent enough to achieve durable virologic control. Some protease inhibitors, in particular those without ritonavir boosting, are not sufficiently effective against HIV-2. Following review of the available evidence and taking the structure and challenges of antiretroviral care in West Africa into consideration, the authors make recommendations and highlight the needs of special populations.
The clustered multikernel: An approach to formal verification of multiprocessor OS kernels

Operating-system kernels are critical software components in computer systems. Building secure, safe and reliable computer systems is facilitated by having strong kernel correctness guarantees. Such guarantees can be obtained by formally verifying a kernel down to the implementation level. Kernel verification has attracted much research interest. For example, the L4.verified project has proved that the implementation of the seL4 microkernel adheres to its formal specification. Nonetheless, due to verification complexity, past research focussed on uniprocessor kernels only. However, with multiprocessor/multicore systems gaining popularity, also in embedded systems, the need for verified multiprocessor kernels arises. To this end, we introduce the clustered multikernel, a point in the design space of multiprocessor kernels. Based on this design, we present a lifting framework, which adds multiprocessor support to a verified uniprocessor kernel and reuses its proofs to obtain a verified multiprocessor kernel with relatively low effort. The lifting framework supports total-store-order (TSO) multiprocessor architectures, which exhibit weak memory ordering. We report on our experience with applying the lifting framework to seL4. All formal specifications and proofs in this work are machinechecked in the interactive theorem prover Isabelle/HOL.
Evaluating educational initiatives to improve palliative care for people with dementia: A narrative review

Dementia accounts for one in three deaths among people aged 65 and over, but end-of-life care for people with dementia is often sub-optimal. Palliative care for people with dementia poses particular challenges to those providing services, and current policy initiatives recommend education and training in palliative care for those working with patients with dementia. However, there are few evaluations of the effectiveness of dementia education and training. This paper presents a narrative review undertaken in 2011–2012 of evaluations of palliative care education for those working with people with dementia at the end of life. A total of eight papers were identified that described and evaluated such palliative care education; none reported benefits for people with dementia. There is a clear need to develop and evaluate educational interventions designed to improve palliative and end-of-life care for people with dementia. Some suggestions for educationally sound approaches are discussed.
A mixed graph model for community detection

A mixed graph theoretic model is proposed for finding communities in a social network. Information on the habits (shopping habits, free time activities) is considered to be known at least for part of the society. The presented model is based on applying parallelly a standard and a bipartite graph. Compared to previous methods, the introduced algorithm has the advantage of noise-tolerance and is suitable independently of the size of the clusters in the graph. Clusters in the dataset tend to form dense subgraphs in both graph models. The idea is to speed up cluster core mining by a modified MST algorithm. Noise in the dataset is defined as missing information on a person's habits. Clustering noisy data is done by using a bipartite graph and fuzzy membership functions. The proposed algorithm can be used for predicting the missing data estimated on the available information patterns. The presented mixed graph model might also be used for image processing tasks.
7.4.1 Coupling Enterprise and Technology by a Compact and Specific Architecture Overview

Enterprise level projects tend to be delayed and to exceed budgets. Original expectations and targets are not met by these projects. Many solutions have been proposed to address this problem, one of them the application of Systems Engineering at large. In this paper we show how a compact Architecture Overview is a helpful instrument to keep enterprise level projects on track.
Thermomechanical analysis of strain localization in a ductile detachment zone

[1] At the latitude of the Thor-Odin dome (British Columbia) the Columbia River Detachment defines the eastern margin of the Shuswap metamorphic core complex and localizes in a 1 km thick muscovite-bearing quartzite mylonite. We present a combined 40Ar/39Ar, (micro)structural, and oxygen isotope study of the deformation history in the detachment and evaluate the spatial and temporal relationships between microstructure formation and localization of strain. High-precision 40Ar/39Ar geochronology from different levels in the mylonite delineates a pattern of increasingly younger (49.0 to 47.9 Ma) deformation ages in deeper levels of the mylonitic footwall. The correlation of 40Ar/39Ar ages with decreasing deformation temperatures (∼550°–400°C) in the top 200 m of the mylonite indicates that deformation migrated downward from the contact with the hanging wall. Strain localization was diachronous in progressively deeper levels of the footwall and was likely controlled by fluid-assisted strain hardening due to advective heat removal and contemporaneous reaction weakening due to dissolution-reprecipitation of white mica. The observed constant high-stress microstructures across the entire detachment indicate that flow stress was buffered by the interplay of strain rate and temperature, where high strain rates at elevated temperature produced the same microstructure as lower strain rates under decreasing temperature conditions. The combined data suggest that the complex interplay among temporally nonuniform rates of footwall exhumation, heat advection, and embrittlement by meteoric fluids strongly determines the thermomechanical behavior of extensional detachments.
MRI Markers of Small Vessel Disease in Lobar and Deep Hemispheric Intracerebral Hemorrhage

Background and Purpose— MRI evidence of small vessel disease is common in intracerebral hemorrhage (ICH). We hypothesized that ICH caused by cerebral amyloid angiopathy (CAA) or hypertensive vasculopathy would have different distributions of MRI T2 white matter hyperintensity (WMH) and microbleeds. Methods— Data were analyzed from 133 consecutive patients with primary supratentorial ICH and adequate MRI sequences. CAA was diagnosed using the Boston criteria. WMH segmentation was performed using a validated semiautomated method. WMH and microbleeds were compared according to site of symptomatic hematoma origin (lobar versus deep) or by pattern of hemorrhages, including both hematomas and microbleeds, on MRI gradient recalled echo sequence (grouped as lobar only–probable CAA, lobar only–possible CAA, deep hemispheric only, or mixed lobar and deep hemorrhages). Results— Patients with lobar and deep hemispheric hematoma had similar median normalized WMH volumes (19.5 cm versus 19.9 cm3, P=0.74) and prevalence of ≥1 microbleed (54% versus 52%, P=0.99). The supratentorial WMH distribution was similar according to hemorrhage location category; however, the prevalence of brain stem T2 hyperintensity was lower in lobar hematoma versus deep hematoma (54% versus 70%, P=0.004). Mixed ICH was common (23%). Patients with mixed ICH had large normalized WMH volumes and a posterior distribution of cortical hemorrhages similar to that seen in CAA. Conclusions— WMH distribution is largely similar between CAA-related and non-CAA-related ICH. Mixed lobar and deep hemorrhages are seen on MRI gradient recalled echo sequence in up to one fourth of patients; in these patients, both hypertension and CAA may be contributing to the burden of WMH.
Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM)

The respiratory system comprises several scales of biological complexity: the genes, cells and tissues that work in concert to generate resultant function. Malfunctions of the structure or function of components at any spatial scale can result in diseases, to the detriment of gas exchange, right heart function and patient quality of life. Vast amounts of data emerge from studies across each of the biological scales; however, the question remains: how can we integrate and interpret these data in a meaningful way? Respiratory disease presents a huge health and economic burden, with the diseases asthma and chronic obstructive pulmonary disease (COPD) affecting over 500 million people worldwide. Current therapies are inadequate owing to our incomplete understanding of the disease pathophysiology and our lack of recognition of the enormous disease heterogeneity: we need to characterize this heterogeneity on a patient-specific basis to advance healthcare. In an effort to achieve this goal, the AirPROM consortium (Airway disease Predicting Outcomes through patient-specific computational Modelling) brings together a multi-disciplinary team and a wealth of clinical data. Together we are developing an integrated multi-scale model of the airways in order to unravel the complex pathophysiological mechanisms occurring in the diseases asthma and COPD.
Scheduling Data Intensive Workloads through Virtualization on MapReduce based Clouds

MapReduce has become a popular programming model for running data intensive applications on the cloud. Completion time goals or deadlines of MapReduce jobs set by users are becoming crucial in existing cloud-based data processing environments like Hadoop. There is a conflict between the scheduling MR jobs to meet deadlines and “data locality” (assigning tasks to nodes that contain their input data). To meet the deadline a task may be scheduled on a node without local input data for that task causing expensive data transfer from a remote node. In this paper, a novel scheduler is proposed to address the above problem which is primarily based on the dynamic resource reconfiguration approach. It has two components: 1) Resource Predictor: which dynamically determines the required number of Map/Reduce slots for every job to meet completion time guarantee; 2) Resource Reconfigurator: that adjusts the CPU resources while not violating completion time goals of the users by dynamically increasing or decreasing individual VMs to maximize data locality and also to maximize the use of resources within the system among the active jobs. The proposed scheduler has been evaluated against Fair Scheduler on virtual cluster built on a physical cluster of 20 machines. The results demonstrate a gain of about 12% increase in throughput of Jobs.