Miracle-dz/UniFAR-FTUs huggingface dataset:
A 2-year study of adjunctive minocycline-HCl in Actinobacillus actinomycetemcomitans-associated periodontitis.

To study the effects of a step-wise treatment regimen on Actinobacillus actinomycetemcomitans-(Aa) associated periodontitis, 4 clusters among 33 patients harboring the organism were followed during successive periods of systemic minocycline plus mechanical debridement and minocycline plus modified Widman flap treatment. Localized periodontitis was found in 2 clusters, one with 7 localized juvenile periodontitis patients and a 24-year old male with localized destruction and extremely low plaque levels (LJP), and the other consisting of 10 patients with plaque and gingivitis and a wider age range (16 to 54 years, LP). Generalized severe and moderate periodontitis was found in 2 clusters which were further discriminated by severe gingivitis and high levels of supragingival plaque (9 patients, GSP), and mild inflammation and low plaque levels (6 patients, GMP). Mean percentages of Aa, as determined by selective cultivation of microbiota from at least 2 periodontal pockets of 6 mm or more were 63, 16, 33, and 7.8% in the clusters (P < 0.01). Six months after active treatment, Aa was present in 6/9 patients and 50% of sites in GSP, and 3/6 patients and 46% of sites in GMP patients. In contrast, the organism was virtually eliminated by scaling and flap procedures in the localized periodontitis clusters, and did not reappear after 6 months (P < 0.05). Combined antibiotic, mechanical, and surgical therapy resulted in a persistence of 20% of sites with residual probing depth of > or = 4 mm in GMP patients after active therapy. At this point, 3 of the GMP patients and 1 GSP patient left the study. Multiple regression analysis showed a significant influence of log-transformed numbers in Aa in cheek and saliva samples at the end of the study, and cluster on the percent residual number of sites with periodontal probing depth of > or = 7 mm (P < 0.001). The present results suggest that the applied therapy would be appropriate in localized forms of Aa periodontitis, but inappropriate in more severe and generalized forms to predictably eliminate Aa. Controlled long-term studies with larger groups of patients will be needed to establish the difference in treatment response suggested by these studies.
Differential Responses of the Coral Host and Their Algal Symbiont to Thermal Stress

The success of any symbiosis under stress conditions is dependent upon the responses of both partners to that stress. The coral symbiosis is particularly susceptible to small increases of temperature above the long term summer maxima, which leads to the phenomenon known as coral bleaching, where the intracellular dinoflagellate symbionts are expelled. Here we for the first time used quantitative PCR to simultaneously examine the gene expression response of orthologs of the coral Acropora aspera and their dinoflagellate symbiont Symbiodinium. During an experimental bleaching event significant up-regulation of genes involved in stress response (HSP90 and HSP70) and carbon metabolism (glyceraldehyde-3-phosphate dehydrogenase, α-ketoglutarate dehydrogenase, glycogen synthase and glycogen phosphorylase) from the coral host were observed. In contrast in the symbiont, HSP90 expression decreased, while HSP70 levels were increased on only one day, and only the α-ketoglutarate dehydrogenase expression levels were found to increase. In addition the changes seen in expression patterns of the coral host were much larger, up to 10.5 fold, compared to the symbiont response, which in all cases was less than 2-fold. This targeted study of the expression of key metabolic and stress genes demonstrates that the response of the coral and their symbiont vary significantly, also a response in the host transcriptome was observed prior to what has previously been thought to be the temperatures at which thermal stress events occur.
Lock-Free Cuckoo Hashing

This paper presents a lock-free cuckoo hashing algorithm, to the best of our knowledge this is the first lock-free cuckoo hashing in the literature. The algorithm allows mutating operations to operate concurrently with query ones and requires only single word compare-and-swap primitives. Query of items can operate concurrently with others mutating operations, thanks to the two-round query protocol enhanced with a logical clock technique. When an insertion triggers a sequence of key displacements, instead of locking the whole cuckoo path, our algorithm breaks down the chain of relocations into several single relocations which can be executed independently and concurrently with other operations. A fine tuned synchronization and a helping mechanism for relocation are designed. The mechanisms allow high concurrency and provide progress guarantees for the data structure's operations. Our experimental results show that our lock-free cuckoo hashing performs consistently better than two efficient lock-based hashing algorithms, the chained and the hopscotch hash-map, in different access pattern scenarios.
Identification and Biochemical Characterization of Two Functional CMP-Sialic Acid Synthetases in Danio rerio*

Background: Addition of sialic acid to the nonreducing end of glycoconjugates requires activation by CMP-sialic acid synthetase (CMAS). Results: In zebrafish, we identified two CMAS enzymes that differ in expression pattern, activities, and intracellular localization. Conclusion: Maintenance of two CMAS paralogues is attributed to subfunctionalization. Significance: Unraveling the individual functions of CMAS paralogues helps to elucidate the impact of sialylation in vertebrate development. Sialic acids (Sia) form the nonreducing end of the bulk of cell surface-expressed glycoconjugates. They are, therefore, major elements in intercellular communication processes. The addition of Sia to glycoconjugates requires metabolic activation to CMP-Sia, catalyzed by CMP-Sia synthetase (CMAS). This highly conserved enzyme is located in the cell nucleus in all vertebrates investigated to date, but its nuclear function remains elusive. Here, we describe the identification and characterization of two Cmas enzymes in Danio rerio (dreCmas), one of which is exclusively localized in the cytosol. We show that the two cmas genes most likely originated from the third whole genome duplication, which occurred at the base of teleost radiation. cmas paralogues were maintained in fishes of the Otocephala clade, whereas one copy got subsequently lost in Euteleostei (e.g. rainbow trout). In zebrafish, the two genes exhibited a distinct spatial expression pattern. The products of these genes (dreCmas1 and dreCmas2) diverged not only with respect to subcellular localization but also in substrate specificity. Nuclear dreCmas1 favored N-acetylneuraminic acid, whereas the cytosolic dreCmas2 showed highest affinity for 5-deamino-neuraminic acid. The subcellular localization was confirmed for the endogenous enzymes in fractionated zebrafish lysates. Nuclear entry of dreCmas1 was mediated by a bipartite nuclear localization signal, which seemed irrelevant for other enzymatic functions. With the current demonstration that in zebrafish two subfunctionalized cmas paralogues co-exist, we introduce a novel and unique model to detail the roles that CMAS has in the nucleus and in the sialylation pathways of animal cells.
Altered sleep homeostasis correlates with cognitive impairment in patients with focal epilepsy

In animal studies, both seizures and interictal spikes induce synaptic potentiation. Recent evidence suggests that electroencephalogram slow wave activity during sleep reflects synaptic potentiation during wake, and that its homeostatic decrease during the night is associated with synaptic renormalization and its beneficial effects. Here we asked whether epileptic activity induces plastic changes that can be revealed by high-density electroencephalography recordings during sleep in 15 patients with focal epilepsy and 15 control subjects. Compared to controls, patients with epilepsy displayed increased slow wave activity power during non-rapid eye movement sleep over widespread, bilateral scalp regions. This global increase in slow wave activity power was positively correlated with the frequency of secondarily generalized seizures in the 3-5 days preceding the recordings. Individual patients also showed local increases in sleep slow wave activity power at scalp locations matching their seizure focus. This local increase in slow wave activity power was positively correlated with the frequency of interictal spikes during the last hour of wakefulness preceding sleep. By contrast, frequent interictal spikes during non-rapid eye movement sleep predicted a reduced homeostatic decrease in the slope of sleep slow waves during the night, which in turn predicted reduced daytime learning. Patients also showed an increase in sleep spindle power, which was negatively correlated with intelligence quotient. Altogether, these findings suggest that both seizures and interictal spikes may induce long-lasting changes in the human brain that can be sensitively detected by electroencephalographic markers of sleep homeostasis. Furthermore, abnormalities in sleep markers are correlated with cognitive impairment, suggesting that not only seizures, but also interictal spikes can have negative consequences.
Globular Head-Displayed Conserved Influenza H1 Hemagglutinin Stalk Epitopes Confer Protection against Heterologous H1N1 Virus

Significant genetic variability in the head region of the influenza A hemagglutinin, the main target of current vaccines, makes it challenging to develop a long-lived seasonal influenza prophylaxis. Vaccines based on the conserved hemagglutinin stalk domain might provide broader cross-reactive immunity. However, this region of the hemagglutinin is immunosubdominant to the head region. Peptide-based vaccines have gained much interest as they allow the immune system to focus on relevant but less immunogenic epitopes. We developed a novel influenza A hemagglutinin-based display platform for H1 hemagglutinin stalk peptides that we identified in an epitope mapping assay using human immune sera and synthetic HA peptides. Flow cytometry and competition assays suggest that the identified stalk sequences do not recapitulate the epitopes of already described broadly neutralizing stalk antibodies. Vaccine constructs displaying 25-mer stalk sequences provided up to 75% protection from lethal heterologous virus challenge in BALB/c mice and induced antibody responses against the H1 hemagglutinin. The developed platform based on a vaccine antigen has the potential to be either used as stand-alone or as prime-vaccine in combination with conventional seasonal or pandemic vaccines for the amplification of stalk-based cross-reactive immunity in humans or as platform to evaluate the relevance of viral peptides/epitopes for protection against influenza virus infection.
Expression level of TBX3 gene in renal carcinoma and its clinical significance

The aim of the current study was to investigate and discuss the function of T-box 3 (TBX3) gene expression in the pathogenesis of renal carcinoma. The carcinoma, adjacent and normal renal tissues of 210 patients with renal carcinoma who presented to The Central Hospital of Wuhan, Tongji Medical College from March, 2006 to March, 2012 were collected to extract total RNAs. The total RNAs were reverse-transcribed into complementary DNA (cDNA), and quantitative polymerase chain reaction (qPCR) was applied to detect the expression of TBX3 gene in these tissues, followed by its association with the prognosis of renal carcinoma as well as clinical features. A comparison of the renal carcinoma tissues with the adjacent tissues showed that TBX3 gene was obviously highly expressed in renal carcinoma tissues (P<0.05). In addition, compared with normal renal tissues, TBX3 gene was obviously highly expressed in renal carcinoma tissues (P<0.05). There was no significant difference in the expression levels of TBX3 gene in normal renal tissues and adjacent tissues (P=0.15). The expression of TBX3 gene in renal carcinoma tissues was not associated with patient age, sex and tumor size (P>0.05), but it was associated with tumor-node-metastasis (TNM) staging and lymph node metastasis (P<0.05). The Kaplan-Meier survival analysis revealed that the median survival time of patients in the positive TBX3 gene expression group (37.5 months) was shorter than that in the negative TBX3 gene expression group (66 months), and there was a statistical difference (P<0.05). The 3- and 5-year survival rates in the negative TBX3 gene expression group were 74 and 62%, respectively, and the 3- and 5-year survival rates in the positive TBX3 gene expression group were 52 and 32%, respectively, and the differences were significant (P<0.05). The results suggest that TBX3 gene is highly expressed in renal carcinoma tissues, and it is associated with TNM staging, lymph node metastasis and distant metastasis, which may be involved in the occurrence and metastasis of renal carcinoma.
Phylogeography Study of Ammodytes personatus in Northwestern Pacific: Pleistocene Isolation, Temperature and Current Conducted Secondary Contact

To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.
Neuropeptide Y regulates a vascular gateway for hematopoietic stem and progenitor cells

Endothelial cells (ECs) are components of the hematopoietic microenvironment and regulate hematopoietic stem and progenitor cell (HSPC) homeostasis. Cytokine treatments that cause HSPC trafficking to peripheral blood are associated with an increase in dipeptidylpeptidase 4/CD26 (DPP4/CD26), an enzyme that truncates the neurotransmitter neuropeptide Y (NPY). Here, we show that enzymatically altered NPY signaling in ECs caused reduced VE-cadherin and CD31 expression along EC junctions, resulting in increased vascular permeability and HSPC egress. Moreover, selective NPY2 and NPY5 receptor antagonists restored vascular integrity and limited HSPC mobilization, demonstrating that the enzymatically controlled vascular gateway specifically opens by cleavage of NPY by CD26 signaling via NPY2 and NPY5 receptors. Mice lacking CD26 or NPY exhibited impaired HSPC trafficking that was restored by treatment with truncated NPY. Thus, our results point to ECs as gatekeepers of HSPC trafficking and identify a CD26-mediated NPY axis that has potential as a pharmacologic target to regulate hematopoietic trafficking in homeostatic and stress conditions.
Transcriptional Activator GmrA, Encoded in Genomic Island OI-29, Controls the Motility of Enterohemorrhagic Escherichia coli O157:H7

Enterohemorrhagic Escherichia coli O157:H7 is a major human enteric pathogen capable of causing large outbreaks of severe infections that induce bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Its genome contains 177 unique O islands (OIs) including those carrying the main virulence elements, Shiga toxin-converting phages (OI-45 and OI-93) and locus for enterocyte effacement (OI-148). However, many of these islands harbor only genes of unknown function. Here, we demonstrate that OI-29 encodes a newly discovered transcriptional activator, Z0639 (named GmrA), that is required for motility and flagellar synthesis in O157:H7. GmrA directly binds to the promoter of fliA, an RNA polymerase sigma factor, and thereby regulates flagellar genes controlled by FliA. Expression of gmrA is maximal under host conditions (37°C, neutral pH, and physiological osmolarity), and in the presence of host epithelial cells, indicative of a role of this gene in infection by promoting motility. Finally, GmrA was found to be a widespread regulator of bacterial motility and flagellar synthesis in different pathotypes of E. coli. Our work largely enriches our understanding of bacterial motility control, and provides another example of regulators acquired laterally that mediate flagellar synthesis.
Endocytic and Recycling Endosomes Modulate Cell Shape Changes and Tissue Behaviour during Morphogenesis in Drosophila

During development tissue deformations are essential for the generation of organs and to provide the final form of an organism. These deformations rely on the coordination of individual cell behaviours which have their origin in the modulation of subcellular activities. Here we explore the role endocytosis and recycling on tissue deformations that occur during dorsal closure of the Drosophila embryo. During this process the AS contracts and the epidermis elongates in a coordinated fashion, leading to the closure of a discontinuity in the dorsal epidermis of the Drosophila embryo. We used dominant negative forms of Rab5 and Rab11 to monitor the impact on tissue morphogenesis of altering endocytosis and recycling at the level of single cells. We found different requirements for endocytosis (Rab5) and recycling (Rab11) in dorsal closure, furthermore we found that the two processes are differentially used in the two tissues. Endocytosis is required in the AS to remove membrane during apical constriction, but is not essential in the epidermis. Recycling is required in the AS at early stages and in the epidermis for cell elongation, suggesting a role in membrane addition during these processes. We propose that the modulation of the balance between endocytosis and recycling can regulate cellular morphology and tissue deformations during morphogenesis.
Effect of scuba diving on the oxidant/antioxidant status, SIRT1 and SIRT3 expression in recreational divers after a winter nondive period

Abstract The aim of this study was to examine the effects of scuba diving on oxidative damage markers in erythrocytes and plasma, antioxidant system in peripheral blood mononuclear cells (PBMCs), as well as sirtuin 1 (SIRT1) and sirtuin 3 (SIRT3) gene expressions in recreational divers after a winter nondive period (at least 5 months). For that purpose, 17 male recreational divers performed an immersion at a depth of 30 m for 30 min. Blood samples were collected immediately before and after diving, 3 and 6 h after diving. Erythrocyte lipid peroxidation measured by thiobarbituric-reactive substances (TBARS) method was significantly increased immediately after diving, but returned to the baseline 6 h after diving, while no significant change was found for plasma TBARS and protein carbonyl derivates in both plasma and erythrocytes. Diving-induced catalase (CAT), superoxide dismutase 2 (SOD2), and consequently total superoxide dismutase (SOD) activities in the PBMC samples (significantly increased immediately after diving, reached the maximum activities 3 h after diving, while 6 h after diving only CAT activity remained significantly increased). No significant change was observed for SOD1 activity and gene expression, as well as SOD2 expression, while CAT and SIRT1 expressions were slightly decreased immediately after diving and 3 h after diving. Interestingly, SIRT3 expression was significantly increased 6 h after diving. In conclusion, after the first dive to 30 m after a nondive season, activation of antioxidant defence was not sufficient to prevent oxidative damage, while SIRT3 upregulation could be a step towards an adaptive response to the diving.
A strategy for human factors/ergonomics: developing the discipline and profession

Human factors/ergonomics (HFE) has great potential to contribute to the design of all kinds of systems with people (work systems, product/service systems), but faces challenges in the readiness of its market and in the supply of high-quality applications. HFE has a unique combination of three fundamental characteristics: (1) it takes a systems approach (2) it is design driven and (3) it focuses on two closely related outcomes: performance and well-being. In order to contribute to future system design, HFE must demonstrate its value more successfully to the main stakeholders of system design. HFE already has a strong value proposition (mainly well-being) and interactivity with the stakeholder group of ‘system actors’ (employees and product/service users). However, the value proposition (mainly performance) and relationships with the stakeholder groups of ‘system experts’ (experts fromtechnical and social sciences involved in system design), and ‘system decision makers’ (managers and other decision makers involved in system design, purchase, implementation and use), who have a strong power to influence system design, need to be developed. Therefore, the first main strategic direction is to strengthen the demand for high-quality HFE by increasing awareness among powerful stakeholders of the value of high-quality HFE by communicating with stakeholders, by building partnerships and by educating stakeholders. The second main strategic direction is to strengthen the application of high-quality HFE by promoting the education of HFE specialists, by ensuring high-quality standards of HFE applications and HFE specialists, and by promoting HFE research excellence at universities and other organisations. This strategy requires cooperation between the HFE community at large, consisting of the International Ergonomics Association (IEA), local (national and regional) HFE societies, and HFE specialists. We propose a joint world-wide HFE development plan, in which the IEA takes a leadership role. Practitioner Summary: Human factors/ergonomics (HFE) has much to offer by addressing major business and societal challenges regarding work and product/service systems. HFE potential, however, is underexploited. This paper presents a strategy for the HFE community to strengthen demand and application of high-quality HFE, emphasising its key elements: systems approach, design driven, and performance and well-being goals.
Tree‐based characterization of low index circuit configurations without passivity restrictions

The present paper addresses index characterizations in differential‐algebraic models of electrical circuits without the need for passivity assumptions. Positive definiteness conditions on the conductance, capacitance and inductance matrices are replaced by certain algebraic assumptions on the so‐called proper trees for augmented node analysis and normal trees for modified node analysis. The current discussion is restricted to index‐0 and index‐1 systems; for the latter, the analysis is based upon certain matrix factorizations which split the topological information from the electrical features of the devices. Several examples illustrate the scope of our framework. Copyright © 2007 John Wiley & Sons, Ltd.