Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation of the annexin 1 counter‐regulatory circuit affords protection in the mouse brain microcirculation

The purpose of this study was to investigate the role of the homeostatic antiinflammatory axis centered on annexin 1 (AnxA1) in cerebral microvascu‐lar dysfunction and tissue injury associated with middle cerebral artery (MCA) occlusion and reperfusion. Intravital fluorescence microscopy was used to visualize the mouse cerebral microcirculation: AnxA1 null mice exhibited more white blood cell adhesion in cerebral venules than their wild‐type counterparts, and this was accompanied by a larger cerebral infarct vol and worse neurological score. All parameters were rescued by delivery of human recombinant AnxA1. To further explore these findings using pharmacological tools, the effect of a short AnxA1 peptidomimetic was tested. When given during the reperfusion phase, peptide Ac2–26 produced similar cerebroprotection, which was associated with a marked attenuation of cell adhesion and markers of inflammation as measured in tissue homogenates. The pharmacological effects of peptide Ac2–26 occurred via receptors of the formyl‐peptide receptor (FPR) family, most likely FPR‐rs2, as deduced by displacement assays with transfected cells and in vivo experiments with transgenic mice and receptor antagonists. Our findings indicate that the endogenous antiinflammatory circuit centered on AnxA1 produces significant cerebral protection, and that these properties might have therapeutic potential for stroke treatment. —Gavins, F. N. E. , Dalli, J., Flower, R. J., Granger, D. N. , Perretti, M. Activation of the annexin 1 counter‐regulatory circuit affords protection in the mouse brain microcirculation FASEB J. 21, 1751–1758 (2007)
Simulation-Optimization In Geographic Maintenance Scheduling

An application of a combination of scheduling theory, simulation modelling and combinatorial optimization is presented. The system under study deals with human resource and assets management to perform maintenance in large support networks. The paper includes the development of the framework of the software tool that will be embedded into the commercial maintenance package called INGRID. Following the modelling approach, a fully detailed explanation of the data requirements, the decision variables and the output variables is given. A detailed discussion on the genetic algorithm that is going to be used is also provided. The routines have been developed in spreadsheets so that there is an easy link with the rest of the software application.
Robust Subspace Segmentation Via Low-Rank Representation

Recently the low-rank representation (LRR) has been successfully used in exploring the multiple subspace structures of data. It assumes that the observed data is drawn from several low-rank subspaces and sometimes contaminated by outliers and occlusions. However, the noise (low-rank representation residual) is assumed to be sparse, which is generally characterized by minimizing the l1-norm of the residual. This actually assumes that the residual follows the Laplacian distribution. The Laplacian assumption, however, may not be accurate enough to describe various noises in real scenarios. In this paper, we propose a new framework, termed robust low-rank representation, by considering the low-rank representation as a low-rank constrained estimation for the errors in the observed data. This framework aims to find the maximum likelihood estimation solution of the low-rank representation residuals. We present an efficient iteratively reweighted inexact augmented Lagrange multiplier algorithm to solve the new problem. Extensive experimental results show that our framework is more robust to various noises (illumination, occlusion, etc) than LRR, and also outperforms other state-of-the-art methods.
Virtual screening reveals a viral-like polymerase inhibitor that complexes with the DNA polymerase of Moniliophthora perniciosa.

The filamentous fungus Moniliophthora perniciosa is a basidiomycota that causes the witches' broom disease in cocoa trees (Theobroma cacao L.). The mitochondrial DNA polymerase of M. perniciosa (MpmitDNApol) is classified within the B family of DNA polymerases, which can be found in viruses and cellular organelles. Using virtual screening processes, accessing KEGG, PubChem, and ZINC databases, we selected the 27 best putative nucleoside viral-like polymerase inhibitors to test against MpmitDNApol. We used Autodock Vina to perform docking simulations of the selected molecules and to return energy values in several ligand conformations. Then, we used Pymol v1.7. 4.4 to check the stereochemistry of chiral carbons, hydrogen bonding receptors, absence or presence of hydrogen, sub and superstructure, numbers of rings, rotatable bonds, and donor groups. We selected the Entecavir Hydrate, a drug used to control hepatitis B; subsequently AMBER 14 was used to describe the behavior of polymerase-entecavir complex after setting up 3500 ps of simulation in water at a temperature of 300 K. From the simulation, a graph of Potential Energy was generated revealing that the ligand remains in the catalytic site after 3500 ps with a final energy of -612,587.4214 kcal/mol.
Authenticated encryption in theory and in practice

Authenticated encryption refers to a class of cryptographic schemes that simultaneously provide message confidentiality and message authenticity. It is an essential component of almost every cryptographic protocol that is used in practice. In this thesis we aim to narrow the gap that exists between authenticated encryption as used in practice, and authenticated encryption as studied in the framework of theoretical cryptography. We examine how certain types of attacks are not captured by the current techniques, and show how this can be remedied by expanding existing security models to capture a wider array of attacks. We begin with a case study of IPsec: a widely deployed security protocol for protecting data across the Internet and other networks. Despite its popularity, IPsec’s security has not received much formal treatment. As a security protocol it offers a relatively high degree of configurability, so as to accommodate multiple usage scenarios. We here present a new set of efficient attacks that fully break the confidentiality of half of the configurations that are permitted by the IPsec standard. Next we turn our attention to the enhancement of security models. In particular we consider attacks that exploit distinguishable decryption failures and ciphertext fragmentation. A number of recent attacks against practical cryptosystems, including our attacks on IPsec, fall in one of these two categories. We extend the current security models to capture such attacks, and formulate new security notions to capture vulnerabilities that arise in this new setting. We then go on to explore how these notions relate to each other, and construct authenticated encryption schemes that satisfy our security notions.
Cuba's exiles: portrait of a refugee migration.

"This article provides a portrait of Cuba's exiles [in the United States] that encompasses all their waves of migration, while utilizing the Cuban exodus to shed light on the broader phenomenon of refugee migration. It argues that to understand the changing social characteristics of the exiles over twenty years of migration, we need to understand the changing phases of the Cuban revolution. Utilizing the Cuban exodus as data, the article uses Egon F. Kunz's.theoretical framework for refugee migration to shed light on the refugees' varying experiences, while also using the actual Cuban refugee experience to react to Kunz's abstract model. "
Trimetazidine, Administered at the Onset of Reperfusion, Ameliorates Myocardial Dysfunction and Injury by Activation of p38 Mitogen-Activated Protein Kinase and Akt Signaling

Trimetazidine [1-(2,3,4-trimethoxybenzyl)piperazine; TMZ] is an anti-ischemic cardiac drug; however, its efficacy and mechanism of cardioprotection upon reperfusion are largely unknown. The objective of this study was to determine whether TMZ, given before reperfusion, could attenuate myocardial reperfusion injury. Ischemia/reperfusion (I/R) was induced in rat hearts by ligating the left anterior descending (LAD) coronary artery for 30 min followed by 48 h of reperfusion. TMZ (5 mg/kg b.wt.) was administered 5 min before reperfusion. The study used three experimental groups: control (−I/R; −TMZ), I/R (+I/R; −TMZ), and TMZ (+I/R; +TMZ). Echocardiography and EPR oximetry were used to assess cardiac function and oxygenation, respectively. The ejection fraction, which was significantly depressed in the I/R group (62 ± 5 versus 84 ± 3% in control), was restored to 72 ± 3% in the TMZ group. Myocardial pO2 in the TMZ group returned to baseline levels (∼20 mm Hg) within 1 h of reperfusion, whereas the I/R group showed a significant hyperoxygenation even after 48 h of reperfusion. The infarct size was significantly reduced in the TMZ group (26 ± 3 versus 47 ± 5% in I/R). TMZ treatment significantly attenuated superoxide levels in the tissue. Tissue homogenates showed a significant increase in p38 and p-Akt and decrease in caspase-3 levels in the TMZ group. In summary, the results demonstrated that TMZ is cardioprotective when administered before reperfusion and that this protection appears to be mediated by activation of p38 mitogen-activated protein kinase and Akt signaling. The study emphasizes the importance of administering TMZ before reflow to prevent reperfusion-mediated cardiac injury and dysfunction.
Comparative proteome analysis of untreated and Helicobacter pylori-treated HepG2.

AIM To investigate the pathological effect of Helicobacter pylori (H pylori) on human hepatic cells, proteomic methods were used to find and to identify proteins that were overexpressed in HepG2 cells treated by H pylori. METHODS H pylori was co-cultured with HepG2 for 6 h. Two-dimensional gel electrophoresis was used to gain the protein expression pattern of untreated and H pylori-treated HepG2. After staining and image analysis, spots of interest were isolated and subjected to mass spectrometry. RESULTS Seven proteins, which were up-regulated in H pylori-treated HepG2 cells, were identified. These proteins included integrin beta-1, protein kinase C alpha, LIM/homeobox protein Lhx1, eIF-2-beta, MAP kinase kinase 3, PINCH protein and Ras-related protein Rab-37, which involved in transcription regulation, signal transduction, metabolism and so on. CONCLUSION H pylori may exert the pathological effect on HepG2 cells by up-regulating the expression of some proteins.
Intelligent clustering guided adaptive prefetching and buffer management for stream processing

Real-time stream data processing is required to handle big data with low latency to process a large amount of incessant streaming data. We propose a clustering based inteligent prefetching scheme and its associated DRAM-PCM (phase change memory) hybrid memory management policy especially for stream processing. To alleviate stream processing's burden of requests accessing main memory, an intelligence prefetching technique is designed to reflect stream processing behavior to reduce the amount of memory access by improving buffer hit ratio. Because stream processing has to guarantee relatively small latency to the users, it is especially important for stream processsing to process the stream data in strict time. By using a hybrid memory structure, we take such advantages like high performance, low energy consumption, and memory scalability. And by using clustering based smart prefetching, we could improve buffer hit rate and because of this, overall system performance can be enhanced. Our proposed architecture and clustering based prefetching method can improve system performance by 1.15 times, compared with hybrid memory and buffer architecture without any prefetching scheme of conventional model and also energy consumption by 1.23 times, compared with DRAM only conventional model.
Predictors of Functional and Quality of Life Outcomes following Deep Brain Stimulation Surgery in Parkinson's Disease Patients: Disease, Patient, and Surgical Factors

Objective The primary objective was to evaluate predictors of quality of life (QOL) and functional outcomes following deep brain stimulation (DBS) in Parkinson's disease (PD) patients. The secondary objective was to identify predictors of global improvement. Methods PD patients who underwent DBS at our Center from 2006 to 2011 were evaluated by chart review and email/phone survey. Postoperative UPDRS II and EQ-5D were analyzed using simple linear regression adjusting for preoperative score. For global outcomes, we utilized the Patient Global Impression of Change Scale (PGIS) and the Clinician Global Impression of Change Scale (CGIS). Results There were 130 patients in the dataset. Preoperative and postoperative UPDRS II and EQ-5D were available for 45 patients, PGIS for 67 patients, and CGIS for 116 patients. Patients with falls/postural instability had 6-month functional scores and 1-year QOL scores that were significantly worse than patients without falls/postural instability. For every 1-point increase in preoperative UPDRS III and for every 1-unit increase in body mass index (BMI), the 6-month functional scores significantly worsened. Patients with tremors, without dyskinesia, and without gait-freezing were more likely to have “much” or “very much” improved CGIS. Conclusions Presence of postural instability, high BMI, and worse baseline motor scores were the greatest predictors of poorer functional and QOL outcomes after DBS.
Predictive motion-field segmentation for image sequence coding

A technique is presented for improving motion field accuracy, while transmitting the same amount of motion information as standard block-based methods (a small amount of additional side information is needed). The approach is developed within the framework of standard block-based methods, but the constraints of the block-based motion field model are relaxed. The method improves motion compensation along boundaries of moving objects by segmenting the motion field of previous frames of the sequence, and using the segmentation to predict the location of motion-field discontinuities in the current frame. Simulations show significant improvement in the accuracy of the motion-compensated frame compared with the standard block-based method and a corresponding decrease in the bit rate required to achieved a fixed image quality. >
Use of Proteinase K Nonspecific Digestion for Selective and Comprehensive Identification of Interpeptide Cross-links: Application to Prion Proteins*

Chemical cross-linking combined with mass spectrometry is a rapidly developing technique for structural proteomics. Cross-linked proteins are usually digested with trypsin to generate cross-linked peptides, which are then analyzed by mass spectrometry. The most informative cross-links, the interpeptide cross-links, are often large in size, because they consist of two peptides that are connected by a cross-linker. In addition, trypsin targets the same residues as amino-reactive cross-linkers, and cleavage will not occur at these cross-linker-modified residues. This produces high molecular weight cross-linked peptides, which complicates their mass spectrometric analysis and identification. In this paper, we examine a nonspecific protease, proteinase K, as an alternative to trypsin for cross-linking studies. Initial tests on a model peptide that was digested by proteinase K resulted in a “family” of related cross-linked peptides, all of which contained the same cross-linking sites, thus providing additional verification of the cross-linking results, as was previously noted for other post-translational modification studies. The procedure was next applied to the native (PrPC) and oligomeric form of prion protein (PrPβ). Using proteinase K, the affinity-purifiable CID-cleavable and isotopically coded cross-linker cyanurbiotindipropionylsuccinimide and MALDI-MS cross-links were found for all of the possible cross-linking sites. After digestion with proteinase K, we obtained a mass distribution of the cross-linked peptides that is very suitable for MALDI-MS analysis. Using this new method, we were able to detect over 60 interpeptide cross-links in the native PrPC and PrPβ prion protein. The set of cross-links for the native form was used as distance constraints in developing a model of the native prion protein structure, which includes the 90–124-amino acid N-terminal portion of the protein. Several cross-links were unique to each form of the prion protein, including a Lys185–Lys220 cross-link, which is unique to the PrPβ and thus may be indicative of the conformational change involved in the formation of prion protein oligomers.
Effects of blood transfusion on oxygen transport variables in severe sepsis

ObjectiveTo investigate whether increasing oxygen delivery (Do2) by increasing hematocrit results in increases in oxygen uptake (Vo2) in septic patients with an abnormal Do2/Vo2 relationship. DesignProspective, randomized, interventional crossover study. SettingTertiary care hospital. PatientsA consecutive sample of 16 patients admitted to the intensive care unit, who were diagnosed as having severe sepsis by defined criteria and who had a hemoglobin concentration of<10 g/dL. InterventionsPatients received, in random order, an infusion of dobutamine (10 μg/kg/min) and a blood transfusion (800 mL of packed red blood cells in 90 mins). Hemodynamic and oxygen transport variables were determined before and after each treatment, allowing at least 20 mins during the infusion of dobutamine to achieve the steady state. Measurements and Main ResultsChanges in Do2 and Vo2 induced by each intervention were measured.Dobutamine significantly increased Do2 (48.5 ± 6.9%; p = .0001) and Vo2 (21.7 ± 3.3%; p = .0001). Blood transfusion increased Do2 (21.4 ± 4.3%; p = .005) but Vo2 did not change significantly (2.2 ± 4.1%). Correlation coefficients for the percent changes of Do2 and Vo2 (r2 = .67 p = .001 for dobutamine; and r2 = 21, p = .07 for blood transfusion) were significantly different for each treatment (p = .0001). ConclusionsIn patients with an abnormal Do2-dependent Vo2, as shown by increases in Vo2 brought about by an infusion of dobutamine, blood transfusion does not significantly increase Vo2, despite significant changes in Do2. The Vo2 in some critically ill patients, depends more on blood flow than on global Do2. (Crit Care Med 1993; 21:1312–1318)
Two Mechanisms of Synaptic Vesicle Recycling in Rat Brain Nerve Terminals

Abstract: KCl and 4‐aminopyridine (4‐AP) evoke glutamate release from rat brain cortical nerve terminals by voltage clamping or by Na+ channel‐generated repetitive action potentials, respectively. Stimulation by 4‐AP but not KCl is largely mediated by protein kinase C (PKC). To determine whether KCl and 4‐AP utilise the same mechanism to release glutamate, we correlated glutamate release with release of the hydrophobic synaptic vesicle (SV) marker FM2‐10. A strong correlation was observed for increasing concentrations of KCl and after application of phorbol 12‐myristate 13‐acetate (PMA) or staurosporine. The parallel increase in exocytosis measured by two approaches suggested it occurred by a PKC‐independent mechanism involving complete fusion of SVs with the plasma membrane. At low concentrations of 4‐AP, alone or with staurosporine, glutamate and FM2‐10 release also correlated. However, higher concentrations of 4‐AP or of 4‐AP plus PMA greatly increased glutamate release but did not further increase FM2‐10 release. This divergence suggests that 4‐AP recruits an additional mechanism of release during strong stimulation that is PKC dependent and is superimposed upon the first mechanism. This second mechanism is characteristic of kiss‐and‐run, which is not detectable by styryl dyes. Our data suggest that glutamate release in nerve terminals occurs via two mechanisms: (1) complete SV fusion, which is PKC independent; and (2) a kiss‐and‐run‐like mechanism, which is PKC dependent. Recruitment of a second release mechanism may be a widespread means to facilitate neurotransmitter release in central neurons.
A performance benchmark and bottleneck analysis of IP multimedia subsystem

IP Multimedia Subsystem (IMS) is an All-IP architecture for telecom networks which provides a layered platform to reduce the costs associated with deployment and delivery of rich multimedia services. Considering the strict service requirements and the large subscriber base of telecom environments, the performance and scalability of IMS would be of critical importance. In this study, with the aim of evaluating the operation of IMS during high workloads, we deployed an IMS test-bed based on the open-source software solutions, and applied extensive performance configurations to the involved subsystems. Then, we conducted benchmark experiments targeting both the IMS control and service layers. The results demonstrate that Home Subscriber Server (HSS) and Serving-Call Session Control Function (S-CSCF) could be potential bottlenecks for performance and scalability of IMS.
Identifying Personal DNA Methylation Profiles by Genotype Inference

Since the first whole-genome sequencing, the biomedical research community has made significant steps towards a more precise, predictive and personalized medicine. Genomic data is nowadays widely considered privacy-sensitive and consequently protected by strict regulations and released only after careful consideration. Various additional types of biomedical data, however, are not shielded by any dedicated legal means and consequently disseminated much less thoughtfully. This in particular holds true for DNA methylation data as one of the most important and well-understood epigenetic element influencing human health. In this paper, we show that, in contrast to the aforementioned belief, releasing one's DNA methylation data causes privacy issues akin to releasing one's actual genome. We show that already a small subset of methylation regions influenced by genomic variants are sufficient to infer parts of someone's genome, and to further map this DNA methylation profile to the corresponding genome. Notably, we show that such re-identification is possible with 97.5% accuracy, relying on a dataset of more than 2500 genomes, and that we can reject all wrongly matched genomes using an appropriate statistical test. We provide means for countering this threat by proposing a novel cryptographic scheme for privately classifying tumors that enables a privacy-respecting medical diagnosis in a common clinical setting. The scheme relies on a combination of random forests and homomorphic encryption, and it is proven secure in the honest-but-curious model. We evaluate this scheme on real DNA methylation data, and show that we can keep the computational overhead to acceptable values for our application scenario.
Regularization for design

An algorithmic bridge is starting to be established between sparse reconstruction theory and distributed control theory. For example, ℓ1-regularization has been suggested as an appropriate means for co-designing sparse feedback gains and consensus topologies subject to performance bounds. In recent work, we showed that ideas from atomic norm minimization could be used to simultaneously co-design a distributed optimal controller and the communication delay structure on which it is to be implemented. While promising and successful, these results lack the same theoretical support that their sparse reconstruction counterparts enjoy - as things stand, these methods are at best viewed as principled heuristics. In this paper, we describe theoretical connections between sparse reconstruction and systems design by developing approximation bounds for control co-design problems via convex optimization.