Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization of a Structure-Specific Resolving Enzyme from Sulfolobus islandicus Rod-Shaped Virus 2

Sulfolobus islandicus rod shaped virus 2 (SIRV2) infects the archaeon Sulfolobus islandicus at extreme temperature (70°C–80°C) and acidity (pH 3). SIRV2 encodes a Holliday junction resolving enzyme (SIRV2 Hjr) that has been proposed as a key enzyme in SIRV2 genome replication. The molecular mechanism for SIRV2 Hjr four-way junction cleavage bias, minimal requirements for four-way junction cleavage, and substrate specificity were determined. SIRV2 Hjr cleaves four-way DNA junctions with a preference for cleavage of exchange strand pairs, in contrast to host-derived resolving enzymes, suggesting fundamental differences in substrate recognition and cleavage among closely related Sulfolobus resolving enzymes. Unlike other viral resolving enzymes, such as T4 endonuclease VII or T7 endonuclease I, that cleave branched DNA replication intermediates, SIRV2 Hjr cleavage is specific to four-way DNA junctions and inactive on other branched DNA molecules. In addition, a specific interaction was detected between SIRV2 Hjr and the SIRV2 virion body coat protein (SIRV2gp26). Based on this observation, a model is proposed linking SIRV2 Hjr genome resolution to viral particle assembly.
Selective Involvement of Serum Response Factor in Pressure-Induced Myogenic Tone in Resistance Arteries

Objective—In resistance arteries, diameter adjustment in response to pressure changes depends on the vascular cytoskeleton integrity. Serum response factor (SRF) is a dispensable transcription factor for cellular growth, but its role remains unknown in resistance arteries. We hypothesized that SRF is required for appropriate microvascular contraction. Methods and Results—We used mice in which SRF was specifically deleted in smooth muscle or endothelial cells, and their control. Myogenic tone and pharmacological contraction was determined in resistance arteries. mRNA and protein expression were assessed by quantitative real-time PCR (qRT-PCR) and Western blot. Actin polymerization was determined by confocal microscopy. Stress-activated channel activity was measured by patch clamp. Myogenic tone developing in response to pressure was dramatically decreased by SRF deletion (5.9±2.3%) compared with control (16.3±3.2%). This defect was accompanied by decreases in actin polymerization, filamin A, myosin light chain kinase and myosin light chain expression level, and stress-activated channel activity and sensitivity in response to pressure. Contractions induced by phenylephrine or U46619 were not modified, despite a higher sensitivity to p38 blockade; this highlights a compensatory pathway, allowing normal receptor-dependent contraction. Conclusion—This study shows for the first time that SRF has a major part to play in the control of local blood flow via its central role in pressure-induced myogenic tone in resistance arteries.
Fast high-performance algorithms for multi-pin droplet routing in digital microfluidic biochips

The use of microfluidics for building biochips is an emerging research area. A key challenge in this area is the droplet routing problem in the design of digital microfluidic biochips. It involves the scheduling of movement of a number of droplets in a time-multiplexed manner to avoid their cross-contamination. This paper attempts to solve this problem for multiple source and target locations with the objectives of minimizing (i) electrode usage, and (ii) latest arrival times. Hierarchical and preferential heuristic algorithms are proposed, and experimental results are observed to be quite encouraging.
Exploring the Effect of Asymmetric Mitochondrial DNA Introgression on Estimating Niche Divergence in Morphologically Cryptic Species

If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.
Mechanism of Action of a Potent Antiplatelet Peptide, Triflavin from Trimeresurus flavoviridis Snake Venom

Summary Triflavin, an antiplatelet peptide from Trimeresurus flavoviridis snake venom, inhibits aggregation of human platelets stimulated by a variety of agonists. However, triflavin does not affect the shape change and release reaction of platelets stimulated by thrombin and collagen. In this paper, we further investigate its effect on the intracellular events occurring after the activation of platelets. Triflavin does not inhibit the intracellular free calcium rise of Quin 2-AM loaded platelets stimulated by thrombin and it also has no significant effect on thromboxane B2 formation of platelets stimulated by thrombin. Triflavin does not affect the 3(H)-inositol monophosphate formation of the 3(H)-myoinositol loaded platelets. However, triflavin dose-dependently inhibits fibrinogen-induced aggregation and 125I-fibrinogen binding of ADP-stimulated platelets. In addition, triflavin dose-dependently blocks fibrinogen-induced aggregation of elastase-treated platelets. It is concluded that triflavin specifically inhibits fibrinogen binding to fibrinogen receptors associated with glycoprotein IIb/IIIa complex on platelet membrane surface without any inhibitory effect on the platelet-activation process.
Stress among medical students.

: Stress is defined as the body’s non-specific response to demands made upon it, or to disturbing events in the environment. It is not just a stimulus or a response but rather, it is a process by which we perceive and cope with environmental threats and challenges. A total of 90 students was included in the study. The mean age of the students was 23.12±2.25 years. There were 50 (56%) females and 40 (44%) males in the study. According to fifteen percent of the students, they do not take stress during their medical studies. Thirty percent of the students responded that, they only take stress during their final examination, that too for difficult subjects only. Fifty five percent of the students responded that they always remain in stress i.e. during routine tests, internal assessments as well as final examinations. A lot of medical students suffer from different levels of stress during their medical studies. The various reasons must be evaluated, and proper policy should be made to minimize this issue.
Socioeconomic inequalities in frailty and frailty components among community-dwelling older citizens

Background So far, it has not yet been studied whether socioeconomic status is associated with distinct frailty components and for which frailty component this association is the strongest. We aimed to examine the association between socioeconomic status and frailty and frailty components. In addition we assessed the mediating effect of the number of morbidities on the association between socioeconomic status and other frailty components. Methods This is a cross-sectional study of pooled data of The Older Persons and Informal Caregivers Survey Minimum DataSet in the Netherlands among community-dwelling persons aged 55 years and older (n = 26,014). Frailty was measured with a validated Frailty Index that consisted of 45 items. The Frailty Index contained six components: morbidities, limitations in activities of daily living (ADL), limitations in instrumental ADL (IADL), health-related quality of life, psychosocial health and self-rated health. Socioeconomic indicators used were education level and neighbourhood socioeconomic status. Results Persons with primary or secondary education had higher overall frailty and frailty component scores compared to persons with tertiary education (P < .001). Lower education levels were most consistently associated with higher overall frailty, more morbidities and worse self-rated health (P < .05 in all age groups). The strongest association was found between primary education and low psychosocial health for persons aged 55–69 years and more IADL limitations for persons aged 80+ years. Associations between neighborhood socioeconomic status and frailty (components) also showed inequalities, although less strong. The number of morbidities moderately to strongly mediated the association between socioeconomic indicators and other frailty components. Conclusion There are socioeconomic inequalities in frailty and frailty components. Inequalities in frailty, number of morbidities and self-rated health are most consistent across age groups. The number of morbidities a person has play an important role in explaining socioeconomic inequalities in frailty and should be taken into account in the management of frailty.
Follicle Microstructure and Innervation Vary between Pinniped Micro- and Macrovibrissae

Histological data from terrestrial, semiaquatic, and fully aquatic mammal vibrissa (whisker) studies indicate that follicle microstructure and innervation vary across the mystacial vibrissal array (i.e. medial microvibrissae to lateral macrovibrissae). However, comparative data are lacking, and current histological studies on pinniped vibrissae only focus on the largest ventrolateral vibrissae. Consequently, we investigated the microstructure, medial-to-lateral innervation, and morphometric trends in harp seal (Pagophilus groenlandicus) vibrissal follicle-sinus complexes (F-SCs). The F-SCs were sectioned either longitudinally or in cross-section and stained with a modified Masson's trichrome stain (microstructure) or Bodian's silver stain (innervation). All F-SCs exhibited a tripartite blood organization system. The dermal capsule thickness, the distribution of major branches of the deep vibrissal nerve, and the hair shaft design were more symmetrical in medial F-SCs, but these features became more asymmetrical as the F-SCs became more lateral. Overall, the mean axon count was 1,221 ± 422.3 axons/F-SC and mean axon counts by column ranged from 550 ± 97.4 axons/F-SC (medially, column 11) to 1,632 ± 173.2 axons/F-SC (laterally, column 2). These values indicate a total of 117,216 axons innervating the entire mystacial vibrissal array. The mean axon count of lateral F-SCs was 1,533 ± 192.9 axons/ F-SC, which is similar to values reported in the literature for other pinniped F-SCs. Our data suggest that conventional studies that only examine the largest ventrolateral vibrissae may overestimate the total innervation by ∼20%. However, our study also accounts for variation in quantification methods and shows that conventional analyses likely only overestimate innervation by ∼10%. The relationship between axon count and cross-sectional F-SC surface area was nonlinear, and axon densities were consistent across the snout. Our data indicate that harp seals exhibit microstructural and innervational differences between their microvibrissae (columns 8-11) and macrovibrissae (columns 1-7). We hypothesize that this feature is conserved among pinnipeds and may result in functional compartmentalization within their mystacial vibrissal arrays.
APOBEC3B deletion impacts on susceptibility to acquire HIV‐1 and its advancement among individuals in western India

APOBEC3B deletion polymorphism has been associated with risk of HIV‐1 acquisition and its progression. Therefore, we aimed to investigate the association of APOBEC3B ins/del polymorphism with risk of acquisition of HIV‐1 and its progression. In the present case–control study, we enrolled a total of 150 HIV‐infected individuals and 150 healthy controls. Polymorphism for APOBEC3B gene was genotyped by PCR. APOBEC3B ID, DD genotypes, and D allele were associated with higher risk of acquisition of HIV‐1 (p = 0.004, OR = 4.96; p = 0.03, OR = 3.55; and p = 0.004; OR = 1.60). The individuals with ID genotypes and combined genotype ID+DD of APOBEC3B in the presence of tobacco and alcohol showed the higher risk of advancement of HIV disease; however, risk could not reach statistical significance (OR = 1.14, 95% CI: 0.59–2.18; OR = 1.33, 95% CI: 0.83–2.15 and OR = 1.44, 95% CI: 0.77–2.69; OR = 1.50, 95% CI: 0.94–2.40). Individuals in advanced HIV disease stage and ID genotype and combined genotype ID + DD of APOBEC3B were more likely to be associated with advanced HIV disease stage but risk could not reach significant (OR = 1.50, 95% CI: 0.94–2.40; OR = 1.27, 95% CI: 0.88–1.84). Individuals with ID and DD genotype of APOBEC3B had influence on susceptibility to acquisition of HIV‐1. This suggests that APOBEC3B deletion may attenuate innate cellular immunity against HIV‐1 and thus confer the host persistence for HIV infection.
Network-centric Actuation Control in Sensor/Actuator Networks based on Bio-inspired Technologies

Self-organization mechanisms have been developed to efficiently operate networked embedded systems. Special focus was given to wireless sensor networks (WSN) and sensor/actuator networks (SANET). Looking at the most pressing issues in such networks, the limited resources and the huge amount of interoperating nodes, the proposed solutions primarily intend to solve the scalability problems by reducing the overhead in data communication. Well-known examples are data-centric routing approaches and probabilistic techniques. In this paper, we intend to go one step further. We are about to also move the operation and control for WSN and SANET into the network. Inspired by the operation of complex biological systems such as the cellular information exchange, we propose a network-centric approach. Our method is based on three concepts: data-centric operation, specific reaction on received data, and simple local behavior control using a policy-based state machine. In summary, these mechanisms lead to an emergent system behavior that allows to control the operation of even large-scale sensor/actuator networks
Self-Organized Discrimination of Resources

When selecting a resource to exploit, an insect colony must take into account at least two constraints: the resource must be abundant enough to sustain the whole group, but not too large to limit exploitation costs, and risks of conflicts with other colonies. Following recent results on cockroaches and ants, we introduce here a behavioral mechanism that satisfies these two constraints. Individuals simply modulate their probability to switch to another resource as a function of the local density of conspecifics locally detected. As a result, the individuals gather at the smallest resource that can host the whole group, hence reducing competition and exploitation costs while fulfilling the overall group's needs. Our analysis reveals that the group becomes better at discriminating between similar resources as it grows in size. Also, the discrimination mechanism is flexible and the group readily switches to a better suited resource as it appears in the environment. The collective decision emerges through the self-organization of individuals, that is, in absence of any centralized control. It also requires a minimal individual cognitive investment, making the proposed mechanism likely to occur in other social species and suitable for the development of distributed decision making tools.
Top Arm Identification in Multi-Armed Bandits with Batch Arm Pulls

We introduce a new multi-armed bandit (MAB) problem in which arms must be sampled in batches, rather than one at a time. This is motivated by applications in social media monitoring and biological experimentation where such batch constraints naturally arise. This paper develops and analyzes algorithms for batch MABs and top arm identification, for both fixed confidence and fixed budget settings. Our main theoretical results show that the batch constraint does not significantly affect the sample complexity of top arm identification compared to unconstrained MAB algorithms. Alternatively, if one views a batch as the fundamental sampling unit, then the results can be interpreted as showing that the sample complexity of batch MABs can be significantly less than traditional MABs. We demonstrate the new batch MAB algorithms with simulations and in two interesting real-world applications: (i) microwell array experiments for identifying genes that are important in virus replication and (ii) finding the most active users in Twitter on a specific topic.
How and why do patients use home blood pressure monitors?

IntroductionLittle is known about how and why patients use home blood pressure monitoring (HBPM). We investigated from where patients obtain their monitor, their reasons for using HBPM, and their frequency of performing blood pressure (BP) measurements. We also examined whether those using HBPM provide written reports of measurements to their doctor and whether they have ever had their monitor checked. MethodsWe conducted a cross-sectional mail survey of adult patients with hypertension enrolled in a practice-based research network of 24 primary care practices throughout the state of North Carolina. We analyzed results using descriptive statistics. ResultsWe received 530 returned questionnaires (76% response rate). Of the 43% (n=226) who reported performing HBPM, 68% purchased their monitor from a pharmacy or department store; the remaining purchased their monitor elsewhere or received it as a gift. Approximately 19% [95% confidence interval (CI): 13.6–23.9] check their BP every day or almost every day; 26% (95% CI: 20.5–32.2) check their BP a few times per week; and 29% (95% CI: 3.0–35.0) check their BP a few times per month.For nearly one-third, their primary reason for using HBPM was because their doctor recommended it. Over one-half said they used HBPM because they were ‘just interested in knowing’ their BP. The majority (70%; 95% CI: 64.4–76.4) indicated that they did not provide a written report of BP readings to their doctor. Less than one-third (29%, 95% CI: 22.9–34.9) has had their monitor checked by a doctor or nurse. ConclusionMost patients with hypertension using HBPM do so because of a doctor's recommendation or a simple desire to know their BP. The majority of those performing home measurements do so at least a few times per month. Most do not provide their doctor with a written report of measurements, and most have not had their monitor checked.
The noble gas concentrations of the Martian meteorites GRV 99027 and paired NWA 7906/NWA 7907

Here we present the isotopic concentrations of He, Ne, Ar, Kr, and Xe for the three Martian meteorites, namely Grove Mountains 99027 (GRV 99027), Northwest Africa 7906 (NWA 7906), and Northwest Africa 7907 (NWA 7907). The cosmic ray exposure (CRE) age for GRV 99027 of 5.7 ± 0.4 Ma (1σ) is consistent with CRE ages for other poikilitic basaltic shergottites and suggests that all were ejected in a single event ~5.6 Ma ago. After correcting for an estimated variable sodium concentration, the CRE ages for NWA 7906 and NWA 7907 of 5.4 ± 0.4 and 4.9 ± 0.4 Ma (1σ), respectively, are in good agreement with the CRE age of ~5 Ma favored by Cartwright et al. ( ) for NWA 7034. The data, therefore, support the conclusion that all three basaltic regolith breccias are paired. The 40Ar gas retention age for NWA 7907 of ~1.3 Ga is in accord with Cartwright et al. ( ). For NWA 7906, we were unable to determine a 40Ar gas retention age. The 4He gas retention ages for NWA 7906 and 7907 are in the range of 200 Ma and are much shorter than the 40Ar gas retention age of NWA 7907, indicating that about 86–88% of the radiogenic 4He has been lost. The Kr and Xe isotopic concentrations in GRV 99027 are composed almost exclusively of Martian interior (MI) gases, while for NWA 7906 and NWA 7907, they indicate gases from the MI, elementally fractionated air, and possibly Martian atmosphere.
Exploring residential characteristics as determinants of environmental sanitation behavior in Ibadan, Nigeria

ABSTRACT This study investigated residential characteristics as determinants of environmental sanitation behavior in Ibadan, Nigeria. The municipality was stratified into three residential zones (core, transition, and suburb). Three political wards were selected in each of the residential zones for questionnaire administration. Using systematic sampling technique, every 20th residential building was selected in the selected wards. Questionnaire was administered in 1,082 residential buildings with a success rate of 84.8% comprising 436 in the core, 351 in the transition, and 295 in the suburb based on the building density in the zones. Focus was on residents with minimum age of 18 years. Findings revealed that environmental sanitation behavior is influenced by residential characteristics such as place of residence, gender, educational attainment, length of residence, household size, and house tenure in Ibadan. All these together can enhance environmental sanitation behavior and preserve sanitary urban environment.
Effect of salmeterol/fluticasone propionate on airway inflammation in COPD: a randomised controlled trial

Background: Airway inflammation in chronic obstructive pulmonary disease (COPD) is characterised by infiltration of CD8+ T cells and CD68+ macrophages and an increased number of neutrophils, whereas few studies have described the presence of eosinophils. Although the anti-inflammatory effects of corticosteroids in stable COPD are unclear, recent studies suggest that combination therapy could be beneficial. A study was therefore undertaken to evaluate combined salmeterol/fluticasone propionate (SFC) and fluticasone propionate (FP) alone on inflammatory cells in the airways of patients with COPD. Methods: Patients were treated in a randomised, double blind, parallel group, placebo-controlled trial with either a combination of 50 µg salmeterol and 500 µg FP twice daily (SFC, n = 19, 19 men, mean age 62 years), 500 µg FP twice daily (n = 20, 15 men, mean age 64 years) or placebo (n = 21, 17 men, mean age 66 years) for 3 months. At the start and end of treatment bronchoscopy with bronchial biopsies was performed and the numbers of CD8+ T lymphocytes, CD68+ macrophages, neutrophils and eosinophils were measured. Results: CD8+ cells were significantly reduced by SFC compared with placebo (difference −98.05 cells/mm2; 95% CI −143.14 to −52.9; p<0.001). Such a marked effect was not seen with FP alone (−44.67 cells/mm2; 95% CI −90.92 to 1.57; p = 0.06). CD68+ macrophages were also reduced by SFC compared with placebo (difference −31.68 cells/mm2; 95% CI −61.07 to −2.29; p = 0.03) but not by FP. SFC did not significantly change neutrophils and eosinophils compared with placebo. Conclusions: SFC has airway anti-inflammatory effects not seen with inhaled corticosteroids alone.