Miracle-dz/UniFAR-FTUs huggingface dataset:
A S L A Hierarchical Computational Model for Distributed Heterogeneous Systems

The Abstract Schema Language (ASL) defines a hierarchical computational model for the development of distributed heterogeneous systems. ASL extends the capabilities and methodologies of concurrent object-oriented programming to enable the construction of highly complex multi-granular systems. The ASL model is described in terms of schemas (concurrent agents), supporting aggregation ( schema assemblages ), and both top-down and bottom-up system designs. ASL encourages code reusability by enabling the integration of heterogeneous components, e.g., procedural and neural network programs. ASL schemas are designed and implemented in an orthogonal fashion; integrated, either statically, through wrapping , or dynamically, via (task) delegation . Schemas include a dynamic interface, made of multiple unidirectional input and output ports, and a body section where schema behavior is specified. Communication is in the form of asynchronous message passing, hierarchically managed, internally, through anonymous port reading and writing, and externally, through dynamic port inter-connections and relabelings.
Pleiotropic effects of fatty acids on pancreatic beta-cells.

Hyperlipidemia is frequently associated with insulin resistance states as found in type 2 diabetes and obesity. Effects of free fatty acids (FFA) on pancreatic beta-cells have long been recognized. Acute exposure of the pancreatic beta-cell to FFA results in an increase of insulin release, whereas a chronic exposure results in desensitization and suppression of secretion. We recently showed that palmitate augments insulin release in the presence of non-stimulatory concentrations of glucose. Reduction of plasma FFA levels in fasted rats or humans severely impairs glucose-induced insulin release. These results imply that physiological plasma levels of FFA are important for beta-cell function. Although, it has been accepted that fatty acid oxidation is necessary for its stimulation of insulin secretion, the possible mechanisms by which fatty acids (FA) affect insulin secretion are discussed in this review. Long-chain acyl-CoA (LC-CoA) controls several aspects of the beta-cell function including activation of certain types of protein kinase C (PKC), modulation of ion channels, protein acylation, ceramide- and/or nitric oxide (NO)-mediated apoptosis, and binding to nuclear transcriptional factors. The present review also describes the possible effects of FA on insulin signaling. We showed for the first time that acute exposure of islets to palmitate upregulates the intracellular insulin-signaling pathway in pancreatic islets. Another aspect considered in this review is the source of FA for pancreatic islets. In addition to be exported to the medium, lipids can be transferred from leukocytes (macrophages) to pancreatic islets in co-culture. This process consists an additional source of FA that may plays a significant role to regulate insulin secretion.
Histone Acetylation in Fungal Pathogens of Plants

Acetylation of histone lysine residues occurs in different organisms ranging from yeast to plants and mammals for the regulation of diverse cellular processes. With the identification of enzymes that create or reverse this modification, our understanding on histone acetylation has expanded at an amazing pace during the last two decades. In fungal pathogens of plants, however, the importance of such modification has only just begun to be appreciated in the recent years and there is a dearth of information on how histone acetylation is implicated in fungal pathogenesis. This review covers the current status of research related to histone acetylation in plant pathogenic fungi and considers relevant findings in the interaction between fungal pathogens and host plants. We first describe the families of histone acetyltransferases and deacetylases. Then we provide the cases where histone acetylation was investigated in the context of fungal pathogenesis. Finally, future directions and perspectives in epigenetics of fungal pathogenesis are discussed.
Did the strategy of skilled attendance at birth reach the poor in Indonesia?

OBJECTIVE To assess whether the strategy of "a midwife in every village" in Indonesia achieved its aim of increasing professional delivery care for the poorest women. METHODS Using pooled Demographic and Health Surveys (DHS) data from 1986-2002, we examined trends in the percentage of births attended by a health professional and deliveries via caesarean section. We tested for effects of the economic crisis of 1997, which had a negative impact on Indonesias health system. We used logistic regression, allowing for time-trend interactions with wealth quintile and urban/rural residence. FINDINGS There was no change in rates of professional attendance or caesarean section before the programmes full implementation (1986-1991). After 1991, the greatest increases in professional attendance occurred among the poorest two quintiles -- 11% per year compared with 6% per year for women in the middle quintile (P = 0.02). These patterns persisted after the economic crisis had ended. In contrast, most of the increase in rates of caesarean section occurred among women in the wealthiest quintile. Rates of caesarean deliveries remained at less than 1% for the poorest two-fifths of the population, but rose to 10% for the wealthiest fifth. CONCLUSION The Indonesian village midwife programme dramatically reduced socioeconomic inequalities in professional attendance at birth, but the gap in access to potentially life-saving emergency obstetric care widened. This underscores the importance of understanding the barriers to accessing emergency obstetric care and of the ways to overcome them, especially among the poor.
Botnet-inspired architecture for interactive spaces

This paper presents a new architecture, Reach4Cloud, for an existing system which allows the building of user friendly interfaces into interactive spaces. Our new system facilitates the controlling of local resources and services using physical user interfaces. In this paper we focus our attention on applying cloud computing architectures used in botnets and malware to our previous distributed computing system. We have identified the command-and-control message bus as the common denominator of botnets. We have also selected the IRC as the message bus and have applied this model as distributed system architecture to a previous version of the system, partially re-architecting it to communicate over the IRC. We have investigated botnets and compare the botnet-based Reach4Cloud system to the original REACHeS architecture while reporting our observations along the way.
Translating the Chronic Care Model Into the Community: Results From a Randomized Controlled Trial of a Multifaceted Diabetes Care Intervention

OBJECTIVE To determine whether using the chronic care model (CCM) in an underserved community leads to improved clinical and behavioral outcomes for people with diabetes. RESEARCH DESIGN AND METHODS This multilevel, cluster-design, randomized controlled trial examined the effectiveness of a CCM-based intervention in an underserved urban community. Eleven primary care practices, along with their patients, were randomized to three groups: CCM intervention (n = 30 patients), provider education only (PROV group) (n = 38), and usual care (UC group) (n = 51). RESULTS A marked decline in HbA(1c) was observed in the CCM group (-0.6%, P = 0.008) but not in the other groups. The magnitude of the association remained strong after adjustment for clustering (P = 0.01). The same pattern was observed for a decline in non-HDL cholesterol and for the proportion of participants who self-monitor blood glucose in the CCM group (non-HDL cholesterol: -10.4 mg/dl, P = 0.24; self-monitor blood glucose: +22.2%, P < 0.0001), with statistically significant between-group differences in improvement (non-HDL cholesterol: P = 0.05; self-monitor blood glucose: P = 0.03) after adjustment. The CCM group also showed improvement in HDL cholesterol (+5.5 mg/dl, P = 0.0004), diabetes knowledge test scores (+6.7%, P = 0.07), and empowerment scores (+2, P = 0.02). CONCLUSIONS These results suggest that implementing the CCM in the community is effective in improving clinical and behavioral outcomes in patients with diabetes.
Stable Lifting construction of non-uniform biorthogonal spline wavelets with compact support

In this paper we use the lifting scheme to construct biorthogonal spline wavelet bases on regularly refined non-uniform grids. The wavelets have at least one vanishing moment and on each resolution level they form an L2 Riesz basis. Furthermore we are interested in determining the exact range of Sobolev exponents for which the complete multilevel system forms a Riesz basis. Hereto we need to examine the smoothness of the dual scaling functions which involves investigation of the spectral properties of the associated transition operator. We provide several examples and discuss their stability. Furthermore we also give a strategy to construct biorthogonal spline wavelets on uniform grids.
Changes of Electrophoretic Protein Profiles of Smoked and Marinated Rainbow Trout (Oncorhynchus mykiss) During Refrigerated Storage

Bu calismayla, tutsulenmis ve marine edilmis gokkusagi alabaliginin (Oncorhynchus mykiss) buzdolabinda depolama suresince elektroforetik protein profilindeki degisimlerin belirlenmesi amaclanmistir. Cig, tutsulenmis ve marine edilmis alabalik orneklerinin, 9 haftalik buzdolabinda depolama suresince kas proteinlerindeki degisimler sodyum dodesil sulfat poliakrilamid jel elektroforezi (SDS-PAGE) kullanilarak incelenmistir. SDS-PAGE ve densitometrik analiz sonuclarina gore, tutsulenmis ve marine edilmis alabalik kaslarinin, aktin bandlarinda onemli bir degisimin olmadigi, buna karsilik bazi protein banlarinin sayisinda ve yogunlugunda bir azalmanin meydana geldigi gozlemlenmistir. Depolamanin 9. haftasinda, 205 kDa molekul agirligindaki myosin agir zinciri (MHC), gozden kaybolmustur. Ayrica tutsulenmis ve marine edilmis orneklerin protein yuzdeleri de haftalik olarak onemli oranda degisim gostermistir (P
Managing data mappings in the Hyperion project

We consider the problem of mapping data in peer-to-peer systems. Such systems rely on simple value searches to locate data of interest. However, different peers may use different values to identify or describe the same data. To accommodate this, peer-to-peer systems often rely on mapping tables that list pairs of corresponding values for search domains that are used in different peers. We illustrate how such tables are used in the genomics community by expert curators. We then argue why mapping tables are appropriate for data mapping in a peer-to-peer environment and motivate the problem of managing these tables. The work presented is part of the Hyperion project.
Cep164, a novel centriole appendage protein required for primary cilium formation

Primary cilia (PC) function as microtubule-based sensory antennae projecting from the surface of many eukaryotic cells. They play important roles in mechano- and chemosensory perception and their dysfunction is implicated in developmental disorders and severe diseases. The basal body that functions in PC assembly is derived from the mature centriole, a component of the centrosome. Through a small interfering RNA screen we found several centrosomal proteins (Ceps) to be involved in PC formation. One newly identified protein, Cep164, was indispensable for PC formation and hence characterized in detail. By immunogold electron microscopy, Cep164 could be localized to the distal appendages of mature centrioles. In contrast to ninein and Cep170, two components of subdistal appendages, Cep164 persisted at centrioles throughout mitosis. Moreover, the localizations of Cep164 and ninein/Cep170 were mutually independent during interphase. These data implicate distal appendages in PC formation and identify Cep164 as an excellent marker for these structures.
Supercomputers and their use in modeling subsurface solute transport modeling

Supercomputers offer a wide range of possibilities for advancing knowledge and solving difficult, real-world problems. Solute transport-related theory and applications have long been an area of specialization within hydrology. In this review, recent applications of supercomputers to solute transport problems are presented. These applications are based mostly on the assumption of a dilute solute, allowing the governing equations to be decoupled. An application of supercomputers is the simulation of solute transport in large heterogeneous spatial domains by both direct solution of the governing equations and by particle- tracking methods. An impetus for this research has been the rapid increase in predictive dispersion models based on analytical stochastic theory. Up until now, relatively few applications have incorporated algorithms designed with a targeted supercomputer in mind, with the result that the machine’s potential cannot be exploited fully. Since many numerical problems are reduced to solutions of algebraic systems when they are implemented on computers, algorithms for linear algebraic systems of equations suitable for vector and parallel machines are discussed in some detail. Data analysis, necessary both for evaluating emerging theories and for more “routine” applications like determining model parameters, is identified as another general area that is ably handled by supercomputers. In particular, supercomputers offer a way to become less dependent on parametric assumptions and constraints, substituting, instead, raw computational power. Visualization techniques and associated facilities have flourished alongside the development of supercomputer centers. These offer the possibility for real-time viewing of solute transport processes, both real and simulated, although little has been produced thus far. It is expected that many more researchers involved with subsurface solute transport will make use of supercomputers in the future.
Parietal epithelial cell activation marker in early recurrence of FSGS in the transplant.

BACKGROUND AND OBJECTIVES Podocyte loss is key in glomerulosclerosis. Activated parietal epithelial cells are proposed to contribute to pathogenesis of glomerulosclerosis and may serve as stem cells that can transition to podocytes. CD44 is a marker for activated parietal epithelial cells. This study investigated whether activated parietal epithelial cells are increased in early recurrent FSGS in transplant compared with minimal change disease. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS CD44 staining in renal allograft biopsies from 12 patients with recurrent FSGS was performed and compared with native kidneys with minimal change disease or FSGS and normal control native and transplant kidneys without FSGS. CD44+ epithelial cells along Bowman's capsule in the parietal epithelial cell location and over the glomerular tuft in the visceral epithelial cell location were assessed. RESULTS Cases with early recurrent FSGS manifesting only foot process effacement showed significantly increased CD44+ visceral epithelial cells involving 29.0% versus 2.6% of glomeruli in minimal change disease and 0% in non-FSGS transplants. Parietal location CD44 positivity also was numerically increased in recurrent FSGS. In later transplant biopsies, glomeruli with segmental lesions had more CD44+ visceral epithelial cells than glomeruli without lesions. CONCLUSIONS Parietal epithelial cell activation marker is significantly increased in evolving FSGS versus minimal change disease, and this increase may distinguish early FSGS from minimal change disease. Whether parietal epithelial cell activation contributes to pathogenesis of sclerosis in idiopathic FSGS or is a regenerative/repair response to replace injured podocytes awaits additional study.
On the Modeling and Analysis of Regulations

Regulations are a wide-spread and important part of government and business. They codify how products must be made and processes should be performed. Such regulations can be difficult to understand and apply. In an environment of growing complexity of, and change in, regulation, automated support for reasoning with regulations is becoming increasingly necessary. In this paper we report on ongoing work which aims at providing automated support for the drafting and use of regulations using logic modelling techniques. We highlight the support that can be provided by logic modelling, describe the technical foundation of our project, and report on the status of the project and the next steps.
Détection de conflits dans les communautés épistémiques en ligne (Conflicts detection in online epistemic communities) [in French]

Conflicts detection in online epistemic communities Conflicts in online epistemic communities can be a blocking factor when producing knowledge. We present a way to automatically detect conflict in Wikipedia discussions, based on subjectivity and connotation marks. Two rules are evaluated : a local rule that uses the structure of the discussion threads, connotation and subjectivity marks and a global rule that takes the whole thread into account and only subjectivity. We show that the two rules produce similar results but that the simplicity of the global rule makes it a preferred approach to detect conflicts.
A light-weight fairness mechanism for chip multiprocessor memory systems

Chip Multiprocessor (CMP) memory systems suffer from the effects of destructive thread interference. This interference reduces performance predictability because it depends heavily on the memory access pattern and intensity of the co-scheduled threads. In this work, we confirm that all shared units must be thread-aware in order to provide memory system fairness. However, the current proposals for fair memory systems are complex as they require an interference measurement mechanism and a fairness enforcement policy for all hardware-controlled shared units. Furthermore, they often sacrifice system throughput to reach their fairness goals which is not desirable in all systems. In this work, we show that our novel fairness mechanism, called the Dynamic Miss Handling Architecture (DMHA), is able to reduce implementation complexity by using a single fairness enforcement policy for the complete hardware-managed shared memory system. Specifically, it controls the total miss bandwidth available to each thread by dynamically manipulating the number of Miss Status Holding Registers (MSHRs) available in each private data cache. When fairness is chosen as the metric of interest and we compare to a state-of-the-art fairness-aware memory system, DMHA improves fairness by 26% on average with the single program baseline. With a different configuration, DMHA improves throughput by 13% on average compared to a conventional memory system.
Pteris latipinna sp. nov. (Pteridaceae), a new species segregated from Pteris fauriei

Abstract Pteris fauriei is widely distributed in Eastern Asia and has high morphological variation. Some morphologically similar plants related to this species are difficult to distinguish. We showed that the new Pteris species from Taiwan, previously identified as P. fauriei, can be morphologically distinguished by its wide pinnae, larger terminal pinnae than the lateral pinnae in sterile fronds, and triangular basal segments of the lateral pinnae. It was confirmed that this species is phylogenetically separated from the other East Asian Pteris species, except for a morphologically distinct species P. arisanensis, by means of chloroplast genes, rbcL and matK. The new species is named as Pteris latipinna sp. nov., referring to its wide pinnae. Here, we provide a key to facilitate the identification of the morphologically similar Pteris species in Asia. The morphological descriptions, images, ecology, and distribution are also presented.
Sex Differences in Tolerability to Anti-Programmed Cell Death Protein 1 Therapy in Patients with Metastatic Melanoma and Non-Small Cell Lung Cancer: Are We All Equal?

BACKGROUND Immune-related adverse events (irAEs) have emerged as a serious clinical issue in the use of immune checkpoint inhibitors (ICIs). Risk factors for irAEs remain controversial. Therefore, we studied sex differences in irAEs in patients treated with anti-programmed cell death protein 1 (PD-1) therapy. MATERIALS AND METHODS All patients with metastatic melanoma and non-small cell lung cancer (NSCLC) treated with anti-PD-1 therapy at Mayo Clinic Rochester and Florida from 2015 to 2018 were reviewed. Kaplan-Meier method and log-rank test was used for time-to-event analysis. RESULTS In 245 patients with metastatic melanoma, premenopausal women were more likely to experience irAEs (all grades) compared with postmenopausal women and men (67% vs. 60% vs. 46%), primarily because of an increase in endocrinopathies (33% vs. 12% vs. 10%, respectively). In patients with NSCLC (231 patients), women (all ages) were also more likely to develop irAEs of all grades (48% vs. 31%). Women with NSCLC were more likely to develop pneumonitis (11% vs. 4%) and endocrinopathies (14% vs. 5%). No differences in grade ≥3 toxicities were seen across sexes in both cohorts, but women were more likely to receive systemic steroids for the treatment of irAEs compared with men. Better progression-free-survival was observed in women with NSCLC and irAEs (10 months vs. 3.3 months) compared with women without irAEs. CONCLUSION Women with metastatic melanoma and NSCLC are more likely to experience irAEs compared with men. We also observed differences between sexes in the frequency of certain irAEs. Larger studies are needed to investigate the mechanisms underlying these associations. IMPLICATIONS FOR PRACTICE The results of this study suggest that women may be at a higher risk for immune-related adverse events (irAEs) compared with men when treated with anti-programmed cell death protein 1 therapy. In addition, women were more likely to develop certain irAEs, including endocrinopathies and pneumonitis. Close follow-up of women undergoing treatment with immune checkpoint inhibitors will allow clinicians to diagnose these treatment-related complications early, potentially reducing their associated morbidity and mortality. In addition, a possible association between irAEs and response to therapy was observed.
Understanding Sequence Similarity and Framework Analysis Between Centromere Proteins Using Computational Biology

Certain mysteries pointing toward their recruitment pathways, cell cycle regulation mechanisms, spindle checkpoint assembly, and chromosome segregation process are considered the centre of attraction in cancer research. In modern times, with the established databases, ranges of computational platforms have provided a platform to examine almost all the physiological and biochemical evidences in disease-associated phenotypes. Using existing computational methods, we have utilized the amino acid residues to understand the similarity within the evolutionary variance of different associated centromere proteins. This study related to sequence similarity, protein–protein networking, co-expression analysis, and evolutionary trajectory of centromere proteins will speed up the understanding about centromere biology and will create a road map for upcoming researchers who are initiating their work of clinical sequencing using centromere proteins.