Miracle-dz/UniFAR-FTUs huggingface dataset:
An (N-1)-resilient algorithm for distributed termination detection

The authors propose a fault-tolerant algorithm for termination detection that can tolerate any number of stop failures. This algorithm improves on existing ones in many aspects, including worst-case message complexity, average-case message complexity and storage overhead. Most important, it runs as efficiently as the best non-fault-tolerant algorithm available if no process fails during the computation, and incurs only a reasonable amount of cost for each process failure that actually occurs. The main idea of the algorithm is a barrier set at a particular process. It is possible that other termination detection algorithms can be made fault-tolerant using similar techniques. <<ETX>>
How are riparian buffer zones around Swedish headwaters implemented

Riparian zones are the transition zones between aquatic and terrestrial environments. They perform numerous important ecological functions. To protect these functions, keeping riparian buffer zones when performing forestry operations around streams is a commonly used practice. In this case study, I investigated how riparian buffer zones around 119 headwaters in northern and southern Sweden are implemented using Rapid Assessment Survey (RAS). I found that 11 % of streams had < 0.1 m wide buffer, 58 % had a buffer 0.1-5 m width, 26 % hade a buffer 5-15 m wide, and 5 % had a buffer wider than 15 m. Northern sites had significantly wider buffers than southern sites. Further, results indicated that neither size of the stream nor size of the clear-cut area influence which buffer width a stream would get. Tree type (coniferous/deciduous) composition of mature trees and saplings of retained buffers differed among buffer width categories and between southern and northern Sweden, and was to some degree a result of the forestry operations within buffers (selective logging). The results also supports that number of deadwood in the stream and shading of the stream are increasing, while the magnitude of impairments connected to forest operations are decreasing, with increasing buffer width. Knowledge of how Swedish headwaters are treated during forest operations, as demonstrated in this study, could help in assessing local effects on small streams due to forest operations as well as cumulative downstream effects on downstream reaches.
Myf5 expression in somites and limb buds of mouse embryos is controlled by two distinct distal enhancer activities

The initiation of skeletal muscle development in the mouse embryo is strictly associated with the expression of the muscle-specific transcription factor Myf5, the first of four myogenic regulatory factors (MRFs) to be expressed in muscle progenitors, and ablation of the Myf5 gene prevents myogenesis. The complex spatiotemporal expression pattern of Myf5 depends on many discrete regulatory elements that are dispersed over long distances throughout the gene locus. These multiple control modules act differently in the various muscle precursor populations, presumably in response to diverse signals that control myogenesis. A potent enhancer region regulating Myf5 expression in limb muscles and somites has been identified previously at –58/–48 kb upstream of the transcriptional start site (Hadchouel et al., 2000). Here, we focus on the physical and functional dissection of this control region. We demonstrate that a conserved sequence of 270 bp located around –57 kb is required and sufficient to drive Myf5 expression in limbs and to maintain it in somites. A second enhancer nearby is responsible for Myf5 transcription in occipital/cranial somites. This enhancer activity also directs expression accurately to the myotome, preventing ectopic expression in the dermomyotome during the second phase of Myf5 gene activation in somites. Our data suggest that the enhancer identified here collaborates with other somitic enhancers to ensure correct myotomal Myf5 expression. Moreover, it constitutes an important element that mediates somitic expression after the initial and transient Myf5 activation through a previously described sonic hedgehog-dependent early epaxial enhancer.
Transcription factor NFAT5 promotes macrophage survival in rheumatoid arthritis

Defective apoptotic death of activated macrophages has been implicated in the pathogenesis of rheumatoid arthritis (RA). However, the molecular signatures defining apoptotic resistance of RA macrophages are not fully understood. Here, global transcriptome profiling of RA macrophages revealed that the osmoprotective transcription factor nuclear factor of activated T cells 5 (NFAT5) critically regulates diverse pathologic processes in synovial macrophages including the cell cycle, apoptosis, and proliferation. Transcriptomic analysis of NFAT5-deficient macrophages revealed the molecular networks defining cell survival and proliferation. Proinflammatory M1-polarizing stimuli and hypoxic conditions were responsible for enhanced NFAT5 expression in RA macrophages. An in vitro functional study demonstrated that NFAT5-deficient macrophages were more susceptible to apoptotic death. Specifically, CCL2 secretion in an NFAT5-dependent fashion bestowed apoptotic resistance to RA macrophages in vitro. Injection of recombinant CCL2 into one of the affected joints of Nfat5+/– mice increased joint destruction and macrophage infiltration, demonstrating the essential role of the NFAT5/CCL2 axis in arthritis progression in vivo. Moreover, after intra-articular injection, NFAT5-deficient macrophages were more susceptible to apoptosis and less efficient at promoting joint destruction than were NFAT5-sufficient macrophages. Thus, NFAT5 regulates macrophage survival by inducing CCL2 secretion. Our results provide evidence that NFAT5 expression in macrophages enhances chronic arthritis by conferring apoptotic resistance to activated macrophages.
Indigenous processing technologies from farm gates adulterate honey quality at local markets and subject consumers to critical health risks

Physico-chemical and microbial status of 400 honey samples picked from 200 experienced apiculturists for laboratory elucidation based on indigenous processing techniques (IPTs) comprising (burning (B); crushing and straining (CS mashing and straining (MS boiling and straining (BS C&S and M&S IPTs resulted to lower FA values (8.10 ± 0.015, 9.50 ± 0.015 and 4.20 ± 0.030) me/kg respectively compared to B&S (10.00 ± 1.00 - 36.67 ± 0.58) me/kg. Greater variation in FA levels confirms the speculations of experts on its fluctuation tendency with honey. Indigenous B gave rise to both highest TRS (31%) and TVMLs (6.95 ± 0.044 cfu/ml). The entire IPTs ubiquitously impacted health threats on honey consumers emanating from microbial contamination. The C&S and M&S IPTs are proved as best honey processing techniques for large scale application at farmgates in Ghana because it conducts the highest counteractive pH to microbial invasions. Innovations on these improved methods could reduce consumer health risks by 90 to 95%.
Modelling and Enforcement of Inter-Process Dependencies with Business Process Modelling Languages

Business process languages have been successfully applied in research and industry for the development of information systems. They are used for the analysis, design, construction, and verifi - cation of software applications and fit well into the model-driven paradigm. Although many business process languages have emerged in the last couple of years, they are in general not used for supporting the integration of existing information systems. In many cases, they are applied for design - ing an integrated system from scratch but less emphasis has been placed on integrating exist ing business process models which would be a natural consequence from a model-driven point of view. In this article we identify inter-process dependencies for the integration of existing business processes and investigate their support from a modelling perspective by currently available business process modelling languages and from an enforcement perspective by an event driven architecture.
International Trends in Sudden Infant Death Syndrome: Stabilization of Rates Requires Further Action

Sudden infant death syndrome (SIDS) is the leading cause of death among infants between 1 month and 1 year of age in the developed world. In the United States, SIDS accounts for 22% of all postneonatal deaths.1 Many countries have launched educational campaigns in an effort to prevent SIDS, focusing on the modifiable factors that had been shown previously to be associated with SIDS.2 Although campaigns vary in the content of their other messages, the leading message of every campaign has been avoidance of the prone position for sleeping infants. Dramatic declines in SIDS have been attributed to these campaigns, which were found to be primarily a result of decreases in prone-sleeping rates.3–9 Other recommendations, such as those advising mothers not to smoke during pregnancy, were followed less widely.3,7 The majority of campaigns were initiated in the late 1980s to early 1990s. In the United States, the American Academy of Pediatrics recommended the nonprone sleeping position for infants in 1992.10 The national Back to Sleep campaign began 2 years later and emphasized the same recommendation.11 In 2000, on the basis of new epidemiologic evidence, the American Academy of Pediatrics recommended back sleeping as the preferred position.7 In the United States, prone-sleeping rates have declined 81%, from 70% in 1992 to 13% in 2005, and supine-sleeping rates have increased from 13% to 72% over that period.12 The US rate of SIDS has declined 55% (from 1.20 in 1000 live births in 199213 to 0.54 in 1000 live births in 2005). 14 Previously, SIDS rates were found to differ by country, as had reductions in rates.15 The purpose of this report is to compare more-recent international data on SIDS and postneonatal infant mortality rates to examine trends, discuss … Address correspondence to Fern R. Hauck, MD, MS, University of Virginia School of Medicine, Department of Family Medicine, PO Box 800729, Charlottesville, VA 22908-0729. E-mail: frh8e{at}virginia.edu
A machine learning information retrieval approach to protein fold recognition

MOTIVATION Recognizing proteins that have similar tertiary structure is the key step of template-based protein structure prediction methods. Traditionally, a variety of alignment methods are used to identify similar folds, based on sequence similarity and sequence-structure compatibility. Although these methods are complementary, their integration has not been thoroughly exploited. Statistical machine learning methods provide tools for integrating multiple features, but so far these methods have been used primarily for protein and fold classification, rather than addressing the retrieval problem of fold recognition-finding a proper template for a given query protein. RESULTS Here we present a two-stage machine learning, information retrieval, approach to fold recognition. First, we use alignment methods to derive pairwise similarity features for query-template protein pairs. We also use global profile-profile alignments in combination with predicted secondary structure, relative solvent accessibility, contact map and beta-strand pairing to extract pairwise structural compatibility features. Second, we apply support vector machines to these features to predict the structural relevance (i.e. in the same fold or not) of the query-template pairs. For each query, the continuous relevance scores are used to rank the templates. The FOLDpro approach is modular, scalable and effective. Compared with 11 other fold recognition methods, FOLDpro yields the best results in almost all standard categories on a comprehensive benchmark dataset. Using predictions of the top-ranked template, the sensitivity is approximately 85, 56, and 27% at the family, superfamily and fold levels respectively. Using the 5 top-ranked templates, the sensitivity increases to 90, 70, and 48%.
Intraoperative lung ultrasound: A clinicodynamic perspective

In the era of evidence-based medicine, ultrasonography has emerged as an important and indispensable tool in clinical practice in various specialties including critical care. Lung ultrasound (LUS) has a wide potential in various surgical and clinical situations for timely and easy detection of an impending crisis such as pulmonary edema, endobronchial tube migration, pneumothorax, atelectasis, pleural effusion, and various other causes of desaturation before it clinically ensues to critical level. Although ultrasonography is frequently used in nerve blocks, airway handling, and vascular access, LUS for routine intraoperative monitoring and in crisis management still necessitates recognition. After reviewing the various articles regarding the use of LUS in critical care, we found, that LUS can be used in various intraoperative circumstances similar to Intensive Care Unit with some limitations. Except for few attempts in the intraoperative detection of pneumothorax, LUS is hardly used but has wider perspective for routine and crisis management in real-time. If anesthesiologists add LUS in their routine monitoring armamentarium, it can assist to move a step ahead in the dynamic management of critically ill and high-risk patients.
How to Train Dependency Parsers with Inexact Search for Joint Sentence Boundary Detection and Parsing of Entire Documents

We cast sentence boundary detection and syntactic parsing as a joint problem, so an entire text document forms a training instance for transition-based dependency parsing. When trained with an early update or max-violation strategy for inexact search, we observe that only a tiny part of these very long training instances is ever exploited. We demonstrate this effect by extending the ArcStandard transition system with swap for the joint prediction task. When we use an alternative update strategy, our models are considerably better on both tasks and train in substantially less time compared to models trained with early update/max-violation. A comparison between a standard pipeline and our joint model furthermore empirically shows the usefulness of syntactic information on the task of sentence boundary detection.
Low Complexity MMSE Vector Precoding Using Lattice Reduction for MIMO Systems

In this paper, a lattice-reduction-aided (LRA) minimum mean square error (MMSE) vector precoding (VP) is proposed for multiple input multiple output (MIMO) systems. Three schemes are provided for the perturbation vector design by Babai's approximation procedures based on lattice reduction method to reduce the complexity. Performance and complexity analysis are provided. Simulation results show that the proposed schemes significantly outperform the conventional MMSE Tomlinson-Harashima precoding (THP) and the zero forcing (ZF) VP. Compared with the MMSE VP via closest-point search, our LRA approach provides a simple alternative with little performance loss.
EFFICACY AND SAFETY OF INTRAVITREAL BEVACIZUMAB COMPARED WITH INTRAVITREAL AND POSTERIOR SUB-TENON TRIAMCINOLONE ACETONIDE FOR TREATMENT OF UVEITIC CYSTOID MACULAR EDEMA

Purpose: To demonstrate the effect of bevacizumab compared with triamcinolone acetonide for the treatment of persistent cystoid macular edema in noninfectious uveitis. Methods: The medical records of 31 eyes of 31 patients with uveitic cystoid macular edema that had persisted despite conventional treatment were reviewed. Ten eyes received 1.25 mg of intravitreal bevacizumab (IVB), 11 eyes received 4 mg of intravitreal triamcinolone acetonide (IVTA), and 10 eyes received 40 mg of posterior sub-Tenon triamcinolone acetonide (PSTA). Changes in visual acuity with a logarithmic minimal angle of resolution and central foveal thickness measured with optical coherence tomography were analyzed. Results: The mean follow-up was 22.3 weeks. The best improvement in visual acuity and reduction in central foveal thickness was achieved at 4 weeks in all groups but worsened with time until 12 weeks (visual acuity improved from baseline by 0.19, 0.27, and 0.16 and central foveal thickness decreased from baseline by 167.4 μm, 327.6 μm, and 166.4 μm with IVB, IVTA, and PSTA, respectively; P < 0.001). The results with IVTA were better than those with IVB or PSTA, although the difference did not reach statistical significance. Intravitreal bevacizumab provided a significantly better effect in visual acuity gain in Behcet uveitis than in non-Behcet uveitis (P = 0.045). Kaplan-Meier survival analysis showed that the median period of effect were 16 weeks with IVB, 30 weeks with IVTA, and 12 weeks with PSTA. An increase in intraocular pressure (>5 mmHg greater than baseline) was observed in 1 eye (10%) with IVB, 5 eyes (45.5%) with IVTA, and 4 eyes (40%) with PSTA. Conclusion: Intravitreal bevacizumab was a well-tolerated and effective supplementary therapy for persistent uveitic cystoid macular edema, especially in Behcet uveitis and for patients with the risk of an increase in intraocular pressure. However, reinjection may be required because of the limited potency and duration of the positive effects of IVB.
Subcortically and callosally projecting neurons are distinct neuronal pools in the motor cortex of the reeler mouse.

Subcortically projecting neurons and callosally projecting ones are distinct neuronal pools in the cerebral cortex of the rodents. However, cortical efferent neurons are known to project multiple targets transiently by plural collateral axons. These plural axons are eliminated during prenatal and postnatal development. In the cerebral cortex of the Reelin-deficient mouse, reeler, which is caused by mutation of the reelin gene, cortical efferent neurons are ectopically distributed. However, it is still unknown whether cortical efferent neurons in the reeler mouse lose surplus collateral axons or maintain them during developmental periods. If surplus collaterals of malpositioned cortical neurons are not eliminated, neurons projecting subcortically may project their axons to the contralateral hemisphere. To test this plausible hypothesis, we made double injections of two fluorescent dyes, Fast Blue and Diamidino yellow dihydrochloride into two of three regions, i.e., upper cervical cord, ventral lateral thalamic nucleus, and contralateral motor cortex of the normal and reeler mice, to label corticospinal, corticothalamic and callosal commissure neurons in the motor cortex, retrogradely. No double labeled neurons were identified in the motor cortex of the normal and reeler mice, although the distribution patterns of these cortical efferent neurons were completely different between normal and reeler mice. These findings strongly suggest that collateral elimination of cortical efferent neurons during developing periods are not affected in this mutant mouse.
Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication

Eukaryotic DNA replication initiates from multiple replication origins. To ensure each origin fires just once per cell cycle, initiation is divided into two biochemically discrete steps: the Mcm2‐7 helicase is first loaded into prereplicative complexes (pre‐RCs) as an inactive double hexamer by the origin recognition complex (ORC), Cdt1 and Cdc6; the helicase is then activated by a set of “firing factors. ” Here, we show that plasmids containing pre‐RCs assembled with purified proteins support complete and semi‐conservative replication in extracts from budding yeast cells overexpressing firing factors. Replication requires cyclin‐dependent kinase (CDK) and Dbf4‐dependent kinase (DDK). DDK phosphorylation of Mcm2‐7 does not by itself promote separation of the double hexamer, but is required for the recruitment of firing factors and replisome components in the extract. Plasmid replication does not require a functional replication origin; however, in the presence of competitor DNA and limiting ORC concentrations, replication becomes origin‐dependent in this system. These experiments indicate that Mcm2‐7 double hexamers can be precursors of replication and provide insight into the nature of eukaryotic DNA replication origins.
Implicit Ingroup Metafavoritism: Subtle Preference for Ingroup Members Displaying Ingroup Bias

The current article investigated how individuals evaluate ingroup members displaying either ingroup bias or egalitarian intergroup behaviors. The hypotheses predicted that on explicit responses a preference for the egalitarian ingroup member would emerge; in contrast, on more spontaneous and uncontrolled responses, a preference for the ingroup favoritist would result. Across four studies these hypotheses were confirmed for both minimal groups (Studies 1 and 2) and ethnic groups (Studies 3 and 4). Despite a verbal preference for those who behaved in an egalitarian way, an implicit ingroup metafavoritism was found. Overall, results indicated the presence of dual attitudes in the perception of ingroup members and the strict interconnection between intergroup behaviors and intragroup perception.
Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides

We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well‐ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A Comparison of the EKF, SPKF, and the Bayes Filter for Landmark-Based Localization

The conventional approach to nonlinear state estimation, the Extended Kalman Filter (EKF), is quantitatively compared to the performance of the relative newcomer, the Sigma-Point Kalman Filter (SPKF). These approaches are applied to the problem of localization of a mobile robot using a known map, and compared under the context of the practical best performance of a Bayes Filter-type method using a particle filter with a very large number of particles.