Miracle-dz/UniFAR-FTUs huggingface dataset:
Functionally specialized junctions between endothelial cells of lymphatic vessels

Recirculation of fluid and cells through lymphatic vessels plays a key role in normal tissue homeostasis, inflammatory diseases, and cancer. Despite recent advances in understanding lymphatic function (Alitalo, K., T. Tammela, and T.V. Petrova. 2005. Nature. 438:946–953), the cellular features responsible for entry of fluid and cells into lymphatics are incompletely understood. We report the presence of novel junctions between endothelial cells of initial lymphatics at likely sites of fluid entry. Overlapping flaps at borders of oak leaf–shaped endothelial cells of initial lymphatics lacked junctions at the tip but were anchored on the sides by discontinuous button-like junctions (buttons) that differed from conventional, continuous, zipper-like junctions (zippers) in collecting lymphatics and blood vessels. However, both buttons and zippers were composed of vascular endothelial cadherin (VE-cadherin) and tight junction–associated proteins, including occludin, claudin-5, zonula occludens–1, junctional adhesion molecule–A, and endothelial cell–selective adhesion molecule. In C57BL/6 mice, VE-cadherin was required for maintenance of junctional integrity, but platelet/endothelial cell adhesion molecule–1 was not. Growing tips of lymphatic sprouts had zippers, not buttons, suggesting that buttons are specialized junctions rather than immature ones. Our findings suggest that fluid enters throughout initial lymphatics via openings between buttons, which open and close without disrupting junctional integrity, but most leukocytes enter the proximal half of initial lymphatics.
Characterization of the binding interface between ubiquitin and class I human ubiquitin-conjugating enzyme 2b by multidimensional heteronuclear NMR spectroscopy in solution.

Ubiquitin-conjugating enzymes (Ubc) are involved in ubiquitination of proteins in the protein degradation pathway of eukaryotic cells. Ubc transfers the ubiquitin (Ub) molecules to target proteins by forming a thioester bond between their active site cysteine residue and the C-terminal glycine residue of ubiquitin. Here, we report on the NMR assignment and secondary structure of class I human ubiquitin-conjugating enzyme 2b (HsUbc2b). Chemical shift perturbation studies allowed us to map the contact area and binding interface between ubiquitin and HsUbc2b by1H-15N HSQC NMR spectroscopy. The serine mutant of the active site Cys88 of HsUbc2b was employed to obtain a relatively stable covalent ubiquitin complex of HsUbc2b(C88S). Changes in chemical shifts of amide protons and nitrogen atoms induced by the formation of the covalent complex were measured by preparing two segmentally labeled complexes with either ubiquitin or HsUbc2b(C88S)15N-labeled. In ubiquitin, the interaction is primarily sensed by the C-terminal segment Val70 - Gly76, and residues Lys48 and Gln49. The surface area on ubiquitin, as defined by these residues, overlaps partially with the presumed binding site with ubiquitin-activating enzyme (E1). In HsUbc2b, most of the affected residues cluster in the vicinity of the active site, namely, around the active site Cys88 itself, the second alpha-helix, and the flexible loop which connects helices alpha2 and alpha3 and which is adjacent to the active site. An additional site on HsUbc2b for a weak interaction with ubiquitin could be detected in a titration study where the two proteins were not covalently linked. This site is located on the backside of HsUbc2b opposite to the active site and is part of the beta-sheet. The covalent and non-covalent interaction sites are clearly separated on the HsUbc2b surface, while no such clear-cut segregation of the interaction area was observed on ubiquitin.
Infrared microspectroscopy of individual human cervical cancer (HeLa) cells.

We report infrared (IR) spectra observed for individual, cultured human cervical cancer (HeLa) cells. Spectra were collected microscopically, in reflection/absorption modes, from cells deposited and dried on microscope slides or from cells grown directly on slides. Within the spectra of the dried cells, significant spectral heterogeneity exists that was previously attributed to different stages of the cell cycle [Boydston-White. S. , et al., Biospectroscopy 1999, 5, 219-227; Holman, H. Y. , et al., Biopolymers Biospectrosc 2000, 57, 329-335; Tobin, M. J., et al., in First BASIE Workshop, Karlsruhe, Germany, 2003]. The results reported here confirm earlier findings and present the possibility of determining the abundance of cells within each stage of the cycle from the IR spectra. In an accompanying paper, we show that the spectra of cells in suspension exhibit spectral intensity distributions that are different from that of the dried cells. This result has far-reaching implications for the use of infrared microspectroscopy to screen dried cell preparations for the presence of abnormal cells.
Information model design as model-driven for Service Oriented Architecture (SOA) implementation in PK-BLU institution using SOA Ontology: Case study: Financial Administration Bureau Padjadjaran University

In implementing good financial management and to be able to maintain the result of the audit report that Padjadjaran University (Unpad) has financial statement with state fair without exception (Wajar Tanpa Pengecualian (WTP)), Unpad should be able to improve the management of financial information to produce quality information. To produce this quality information Unpad should be integrated the exisisting information systems and distribute information with ease of access. But it cannot be implemented as long as the information systems have not been able to communicate and distribute information to each other. Service Oriented Architecture (SOA) offers a solution to meet the needs in the use of the services that run on applications and information systems in an architecture that can run in unintegrated environments and environments with different platform. In implementing SOA, understanding the core concepts of SOA need to be equated for all parties involved in the design and implementation of SOA, so the grouping and defining the services that running in financial management at Unpad conducted by the Biro Administrasi Keuangan did not experience obstacles and barriers. In this study researched the design of financial management information model that is consistent with the core concept of SOA implementation, the modeling approach to information designed using conceptual framework SOA Ontology, wich is one of SOA standards, published by the Open Group. Designing information models done with an object-oriented approach, this approach defines each function and actors as classes. With object-oriented approach is in accordance with the conceptual framework SOA Ontology is also used in describing the class diagram notation of the core concepts of SOA. This study is qualitative research procedure uses strategy of inquiry using a case study on Biro Administrasi Keuangan (financial administration bureau). The information model is expected to deliver Unpad in designing, building, and implementing SOA at Unpad.
Glutamate, NMDA, and AMPA Induced Changes in Extracellular Space Volume and Tortuosity in the Rat Spinal Cord

Glutamate release, particularly in pathologic conditions, may result in cellular swelling. The authors studied the effects of glutamate, N-methyl-d-aspartate (NMDA), and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) on extracellular pH (pHe), extracellular potassium concentration ([K+]e), and changes in extracellular space (ECS) diffusion parameters (volume fraction α, tortuosity λ) resulting from cellular swelling. In the isolated spinal cord of 4-to 12-day-old rats, the application of glutamate receptor agonists induced an increase in [K+]e, alkaline-acid shifts, a substantial decrease in α, and an increase in λ. After washout of the glutamate receptor agonists, α either returned to or overshot normal values, whereas λ remained elevated. Pretreatment with 20 mmol/L Mg++, MK801, or CNQX blocked the changes in diffusion parameters, [K+]e and pHe evoked by NMDA or AMPA. However, the changes in diffusion parameters also were blocked in Ca2+-free solution, which had no effect on the [K+]e increase or acid shift. The authors conclude that increased glutamate release may produce a large, sustained and [Ca2+]e-dependent decrease in α and increase in λ. Repetitive stimulation and pathologic states resulting in glutamate release therefore may lead to changes in ECS volume and tortuosity, affecting volume transmission and enhancing glutamate neurotoxicity and neuronal damage.
liteDTW: A lightweight dynamic time warping for tiny wireless sensing devices

Wireless sensor networks have been recognized as promising tools to collect relevant, in-situ data for a wide range of application domains. However, such networks suffer from hard constraints including the allocated resources. Hence, current research endeavors strive to minimize the amount of data that has to be transmitted. This is typically achieved via data fusing or sending some nodes to sleep mode whenever their readings exhibit a high degree of spatio/temporal correlation. Accordingly, the degree of correlation can be considered as a metrics for data filtering. The Dynamic time warping (DTW) algorithm is a "natural" candidate for data fusion and correlation estimation at intermediate sensor nodes via matching the various measured readings. However, the DTW algorithm suffers from the excessive computational overhead which is ill-suited for the "resources-taxed" sensor nodes. This work aims at reducing this burden via refining the implementation procedure of the DTW algorithm. The liteDTW is a novel version of the DTW algorithm with linear operations and fuzzy abstraction. The core idea is to reduce the DTW matrix dimensions via shrinking the input patterns. Several simulations and real experiments have been conducted to validate that the liteDTW algorithm excels over the naive one in terms of accuracy, time and space overhead. Moreover, the Cooja simulator of the Contiki OS has been utilized to assess the energy profit of adopting the liteDTW algorithm for data fusion.
Rationale, Methodology, and Implementation of a Dispatcher-assisted Cardiopulmonary Resuscitation Trial in the Asia-Pacific (Pan-Asian Resuscitation Outcomes Study Phase 2)

Abstract Background. Survival outcomes from out-of-hospital cardiac arrest (OHCA) in Asia are poor (2–11%). Bystander cardiopulmonary resuscitation (CPR) rates are relatively low in Asia. Dispatcher-assisted CPR (DA-CPR) has recently emerged as a potentially cost-effective intervention to increase bystander CPR and survival from OHCA. The Pan-Asian Resuscitation Outcomes Study (PAROS), an Asia-Pacific cardiac arrest registry, was set up in 2009, with the aim of understanding OHCA as a disease in Asia and improving OHCA survival. The network has adopted DA-CPR as part of its strategy to improve OHCA survival. Objective. This article aims to describe the conceptualization, study design, potential benefits, and difficulties for implementation of DA-CPR trial in the Asia-Pacific. Methods. Two levels of intervention, basic and comprehensive, will be offered to PAROS participating sites. The basic level consists of implementation of a DA-CPR protocol and training program, while the comprehensive level consists of implementation of the basic level, with the addition of a dispatch quality measurement tool, quality improvement program, and community education program. Sites that are not able to implement the package will contribute control data. The primary outcome of the study is survival to hospital discharge or survival to 30 days post cardiac arrest. DA-CPR and bystander CPR are secondary outcomes. Conclusion. Implementation of DA-CPR requires concerted efforts by EMS leaders and supervisors, dispatchers, hospital stakeholders, policy makers, and the general public. The DA-CPR trial implemented by the PAROS sites, if successful, can serve as a model for other countries considering such an intervention in their EMS systems.
CSX/Nkx2.5 Modulates Differentiation of Skeletal Myoblasts and Promotes Differentiation into Neuronal Cells in Vitro*

CSX/Nkx2.5 transcription factor plays a pivotal role in cardiac development; however, its role in development and differentiation of other organs has not been investigated. In this study, we used C2C12 myoblasts and human fetal primary myoblasts to investigate the function of Nkx2.5 in skeletal myogenesis. The expression levels of Nkx2.5 decreased as C2C12 myoblasts elongated and fused to form myotubes. The expression of human NKX2.5 in C2C12 myoblasts inhibited myocyte differentiation and myotube formation, and up-regulated Gata4 and Tbx5 expression. The expression of NKX2.5 in terminally differentiated C2C12 myotubes resulted in a change in morphology and breakdown into smaller myotubes. Furthermore, overexpression of NKX2.5 in C2C12 cells and primary cultures of human fetal myoblasts led to differentiation of myoblasts into neuron-like cells and expression of neuronal markers. This study sheds light on the previously unknown non-cardiac functions of Nkx2.5 transcription factor.
Contribution of the Shigella flexneri Sit, Iuc, and Feo Iron Acquisition Systems to Iron Acquisition In Vitro and in Cultured Cells

ABSTRACT Shigella flexneri possesses multiple iron acquisition systems, including proteins involved in the synthesis and uptake of siderophores and the Feo system for ferrous iron utilization. We identified an additional S. flexneri putative iron transport gene, sitA, in a screen for S. flexneri genes that are induced in the eukaryotic intracellular environment. sitA was present in all Shigella species and in most enteroinvasive Escherichia coli strains but not in any other E. coli isolates tested. The sit locus consists of four genes encoding a potential ABC transport system. The deduced amino acid sequence of the S. flexneri sit locus was homologous to the Salmonella enterica serovar Typhimurium Sit and Yersinia pestis Yfe systems, which mediate both manganese and iron transport. The S. flexneri sit promoter was repressed by either iron or manganese, and the iron repression was partially dependent upon Fur. A sitA::cam mutation was constructed in S. flexneri. The sitA mutant showed reduced growth, relative to the wild type, in Luria broth containing an iron chelator but formed wild-type plaques on Henle cell monolayers, indicating that the sitA mutant was able to acquire iron and/or manganese in the host cell. However, mutants defective in two of these iron acquisition systems (sitA iucD, sitA feoB, and feoB iucD) formed slightly smaller plaques on Henle cell monolayers. A strain carrying mutations in sitA, feoB, and iucD did not form plaques on Henle cell monolayers.
Formal Methods for Intellectual Property Composition Across Synchronization Domains

A significant part of the System-on-a-Chip (SoC) design problem is in the correct composition of intellectual property (IP) blocks. Ever increasing clock frequencies make it impossible for signals to reach from one end of the chip to the other end within a clock cycle; this invalidates the so-called synchrony assumption, where the timing of computation and communication are assumed to be negligible, and happen within a clock cycle. Missing the timing deadline causes this violation, and may have ramifications on the overall system reliability. Although latency insensitive protocols (LIPs) have been proposed as a solution to the problem of signal propagation over long interconnects, they have their own limitations. A more generic solution comes in the form of globally asynchronous locally synchronous (GALS) designs. However, composing synchronous IP blocks either over long multicycle delay interconnects or over asynchronous communication links for a GALS design is a challenging task, especially for ensuring the functional correctness of the overall design. In this thesis, we analyze various solutions for solving the synchronization problems related with IP composition. We present alternative LIPs, and provide a validation framework for ensuring their correctness. Our notion of correctness is that of latency equivalence between a latency insensitive design and its synchronous counterpart. We propose a trace-based framework for analyzing synchronous behaviors of different IPs, and provide a correct-by-construction protocol for their transformation to a GALS design. We also present a design framework for facilitating GALS designs. In the framework, Kahn process network specifications are refined into correct-by-construction GALS designs. We present formal definitions for the refinements towards different GALS architectures. For facilitating GALS in distributed embedded software, we analyze certain subclasses of synchronous designs using a Pomset-based semantic model that allows for desynchronization toward GALS. * *This project received support from CCF-0417340 (CRCD), CCF-0237947 (CAREER), and CCF-0702316 (NSF).
Venation pattern formation in Arabidopsis thaliana vegetative leaves.

Branching net-like structures are a trait common to most multicellular organisms. However, our knowledge is still poor when it comes to the genetic operations at work in pattern formation of complex network structures such as the vasculature of plants and animals. In order to initiate a causal analysis of venation pattern formation in dicotyledonous plant leaves, we have first studied its developmental profile in vegetative leaves of a wild-type strain of the model organism Arabidopsis thaliana. As landmarks of the complexity of the venation pattern, we have defined three main developmental parameters, which have been quantitatively followed in time: the ratios of (a) the length and (b) the number of branchpoints of the vein network with the surface of the lamina, which decrease in parallel as the leaf grows, only small differences existing between successive leaves, and (c) the number of hydathodes per leaf, which increases both during leaf expansion and from juvenile to adult rosette leaves. We next searched for natural variations in the first vegetative leaves of 266 ecotypes, finding only 2 which showed a venation pattern unequivocally different from that of the rest, Ba-1 and Ei-5, the latter displaying an extremely simple pattern that we have called Hemivenata. This phenotype, which is inherited as a monogenic recessive trait, is visible both in leaves and in cotyledons and seems to arise from a perturbation in an early acting patterning mechanism. Finally, we have screened for mutants with abnormal venation pattern but normally shaped leaves, concluding that such a phenotype is rare, since only one recessive mutation was obtained, extrahydathodes, characterized by the presence of an increased number of hydathodes per leaf.
Interactions between NKG2x Immunoreceptors and HLA-E Ligands Display Overlapping Affinities and Thermodynamics1

The NKG2x/CD94 family of C-type lectin-like immunoreceptors (x = A, B, C, E, and H) mediates surveillance of MHC class Ia cell surface expression, often dysregulated during infection or tumorigenesis, by recognizing the MHC class Ib protein HLA-E that specifically presents peptides derived from class Ia leader sequences. In this study, we determine the affinities and interaction thermodynamics between three NKG2x/CD94 receptors (NKG2A, NKG2C, and NKG2E) and complexes of HLA-E with four representative peptides. Inhibitory NKG2A/CD94 and activating NKG2E/CD94 receptors bind HLA-E with indistinguishable affinities, but with significantly higher affinities than the activating NKG2C/CD94 receptor. Despite minor sequence differences, the peptide presented by HLA-E significantly influenced the affinities; HLA-E allelic differences had no effect. These results reveal important constraints on the integration of opposing activating and inhibitory signals driving NK cell effector functions.
Non-linear Optimization of Performance Functions for Autonomic Database Performance Tuning

Modern ondemand environments are coined by a heterogeneous diversity of components, architectures and applications. High performance, availability and further service level agreements need to be satisfied under any circumstances in order to please customers. Today, highly skilled database administrators (DBAs) are required to tune the DBMS within their complex environments. Achieved DBMS' performance depends on individual DBA skills, home-grown tuning scripts and in most cases is reactive to obvious and urgent performance problems. This paper addresses the idea of classifying, formalizing, obtaining, storing, maintaining, exchanging and individually adapting DBA expert tuning-knowledge as shared domain of understanding in the autonomic management process. Hereby, we focus our attention on the development of a resource dependency model that allows for (precise) optimization and decision-support at run-time, in contrast to traditional trial-and- error, feedback-based tuning methodologies based on best- practices.
Poverty and Shared Prosperity: Let’s Move the Discussion Beyond Growth*

Abstract Some authors argue that it is enough to focus on growth to achieve lower poverty and greater shared prosperity. Policy-makers are warned that any effort to make growth more equal would be a distraction at best and could even be detrimental. Achieving the World Bank target of a 3% poverty rate by 2030 will require, however, more targeted policies favoring the poorest segments of the population. But what would be these policies? While studies investigating determinants of GDP growth have been numerous, less is known about factors influencing household incomes at the lowest segments of the income distribution. This paper estimates income drivers for the poorest two income quintiles drawing on a panel of 117 countries over the period 1967–2011. Its results suggest that maintaining macroeconomic stability as well as investing in human and physical capital would not only be associated with faster overall economic growth, but also with even faster income growth for the poorest segments of the population. This paper confirms the central role overall economic growth should play in any strategy to reduce poverty. Its results suggest, however, that in addition policy-makers may have instruments to tweak the distribution of the benefits of faster economic growth in favor of the households at the bottom of the income distribution. There thus need not be a trade-off between inequality and growth.
[Analysis of genetic relationships of Pueraria thomsonii based on SRAP markers].

OBJECTIVE To determine the interspecies relationships of 18 Pueraria thomsonii cultivars in molecular level. METHOD Eighteen P. thomsonii cultivars were evaluated by using sequence-related amplified polymorphism (SRAP) markers, with P. lobata and P. peduncularis as contrast species. Systematic relationships were constructed based on the UPGMA method by TREECONW software. RESULT The results showed that 22 primer pairs produced 338 loci, out of which 216 were polymorphic, the percentage of polymorphic loci was 63.9%. An average of 15.4 loci and 9.8 polymorphic loci were generated by each pair of primers. Genetic distance was analyzed by TREECONW software. Genetic distance of 18 P. thomsonii were changed from 0.004 7 to 0.265 8, with an average of 0.316. Using cluster analysis (UPGMA) based on those polymorphism bands amplified with SRAP primers, the 22 cultivars were classified into three groups, groups 1 with 18 P. thomsonii, group 2 with 3 P. lobata, and group 3 with 1 P. peduncularis. Most of the P. thomsonii from the same region were not in the same group. CONCLUSION SRAP markers could be a good marker for genetic relationship research in the P. thomsonii.