Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

Background Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis. Principal Findings Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs. Conclusion The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may aid development of LTR-targeted pharmaceuticals.
Comparison between two shock wave regimens using frequencies of 60 and 90 impulses per minute for urinary stones

PURPOSE: Two different regimens of SWL delivery for treating urinary stones were compared. METHODS: Patients with urinary stones were randomly divided into two groups, one of which received 3000 shocks at a rate of 60 impulses per minute and the other of which received 4000 shocks at 90 impulses per minute. Success was defined as stone‐free status or the detection of residual fragments of less than or equal to 3 mm three months after treatment. Partial fragmentation was considered to have occurred if a significant reduction in the stone burden was observed but residual fragments of 3mm or greater remained. RESULTS: A total of 143 procedures were performed with 3000 impulses at a rate of 60 impulses per minute, and 156 procedures were performed with 4000 impulses at 90 impulses per minute. The stone‐free rate was 53.1% for patients treated with the first regimen and 54.8% for those treated with the second one (p = 0.603). The stone‐free rate for stones smaller than 10 mm was 60% for patients treated with 60 impulses per minute and 58.6% for those treated with 90 impulses per minute. For stones bigger than 10 mm, stone‐free rates were 34.2% and 45.7%, respectively (p = 0.483). Complications occurred in 2.3% of patients treated with 60 impulses per minute and 3.3% of patients treated with 90 impulses per minute. CONCLUSION: No significant differences in the stone‐free and complication rates were observed by reducing the total number of impulses from 4000 to 3000 and the frequency from 90 to 60 impulses per minute.
Glycaemic control and C- reactive protein levels in type 2 diabetes mellitus -how well they co-relate?: a prospective study

Background: Poorly controlled diabetes mellitus as indicated by elevated glycated haemoglobin (HbA1c) levels is associated with increased cardiovascular risk. C–reactive protein (CRP), an important cardiovascular risk factor, is elevated in diabetics with poor glycaemic control than those with good control. The present study assessed the correlation between HbA1c and CRP levels.Methods: A prospective study was conducted in thirty type 2 diabetic patients irrespective of the disease duration and treatment; those with established target organ damage were excluded. HbA1c and hsCRP levels were measured at baseline; sugars were monitored monthly and medications optimised; at the end of six months HbA1c and hsCRP levels were measured.Results: Mean age of the study subjects was 58.7±8.6 years; At the baseline, all had poor glycaemic control (HbA1c >7%); 15 had hsCRP >3 mg/L. At the end of 6 months, 5 achieved good glycaemic control (HbA1c <7%); 10 had hsCRP >3 mg/L. Baseline median hsCRP was 3.33 mg/L (0.68, 15.9) and at the end of 6 months it was 2.08 mg/L (0.48, 9.12). Mean HbA1c at baseline and end line was 10.6±1.55% and 8.43±1.84% respectively. There was significant reduction in both the mean HbA1c and median hsCRP at the end of 6 months (p <0.001). Positive correlation was observed between HbA1c and CRP at baseline (r=0.32, p=0.10). However, this was not observed at the end of 6 months.Conclusions: There is positive correlation between the level of glycaemic control (HbA1c) and CRP levels; Better glycaemic control results in significant reduction in the hsCRP levels.
Massive Concha Bullosa with Secondary Maxillary Sinusitis

Concha bullosa is a common anatomic variation of the middle turbinate; however, sinusitis secondary to the concha bullosa is rare. A 52-yr-old woman presented with nasal obstruction and posterior nasal drip. Computed tomography and examination of the nasal cavity revealed septal deviation on the left side, and a massive concha bullosa and maxillary sinusitis on the right side. The lateral lamella of the affected turbinate was removed and the inspissated material was drained. Histopathologic examination of the excised lesion in the concha bullosa revealed bacterial colonies in the mucus plug. We report here on a massive concha bullosa with secondary maxillary sinusitis.
Teacher Sustenance of Emotional Balance among Children aged 4-6 with Disability in Kenya: Addressing Safety, Actualization and Independence.

Teacher management of individual’s physical and psychological wellbeing of learners tend to deliver them from pessimistic and traumatic life threatening circumstances in which children with disabilities (CWD) find themselves particularly between ages 4-6 in Early Childhood Education (E.C.E) centres . The pessimistic and traumatic episodes creates emotional imbalance in children with disabilities particularly navigating around their safety, self actualization and independence in participation in school and community-based activities. Although teachers are instrumental in developing and creating positive relationships necessary for effective participation of CWD, Safety, actualization and independence is often not addressed resulting in frustration, neglect and negative perception which lower inclusion in the learning process. This study assessed teacher sustenance of emotional balance of preschool children aged 4-6 with disability in Nairobi County, Kenya, addressing Safety, Actualization and Independence. Descriptive research design was used to gather data. Target population was 153 preschool teachers, 102 head teachers and 150 preschool with CWD. Purposive and simple random samplings were used. Analysis was obtained through editing, coding classifying and tabulation. The study found inadequacies in emotional stability of CWD. In order to mitigate inadequacies, teachers should supplement core practices with interventions such as providing culturally relevant curricular that reflects experiences for CWD to experience love, joy, acceptance and optimism, create healthy inclusive learning environments and demonstrate appropriate pedagogy for CWD as well as establish and maintain positive relationships. The study recommends the government to adhere to principles of CRPP and CRC, and address barriers to effective participation as well emotional adjustment of CWD.
Comparison of cardiac monophasic action potentials recorded by intracellular and suction electrodes.

The action potentials recorded from heart muscle with a suction electrode have been compared to those recorded with an intracellular microelectrode. It has been found that if the suction electrode is properly used the monophasic potentials recorded with it may be taken as a reliable index of the time of arrival of excitation at the electrode and as a reliable index of the shape of the action potential during the entire phase of repolarization. The suction electrode potentials differ from the microelectrode potentials in showing a lower rise velocity, a smaller amplitude, a quantitatively different reversal or overshoot and, in the beating heart, ‘afterpotentials’ caused by mechanical effects. When the shape of the action potential, as observed with the microelectrode, is changed by ions such as K+ or Ca++ a similar change is observed in the potential recorded with the suction electrodes.
The MERL/MELCO/TUM system for the REVERB Challenge using Deep Recurrent Neural Network Feature Enhancement

This paper describes our joint submission to the REVERB Challenge, which calls for automatic speech recognition systems which are robust against varying room acoustics. Our approach uses deep recurrent neural network (DRNN) based feature enhancement in the log spectral domain as a single-channel front-end. The system is generalized to multi-channel audio by performing single-channel feature enhancement on the output of a sum-and-delay beamformer with direction of arrival estimation. On the back-end side, we employ a state-of-the-art speech recognizer using feature transformations, utterance based adaptation, and discriminative training. Results on the REVERB data indicate that the proposed front-end provides acceptable results already with a simple clean trained recognizer while being complementary to the improved back-end. The proposed ASR system with eight-channel input and feature enhancement achieves average word error rates (WERs) of 7.75 % and 20.09 % on the simulated and real evaluation sets, which is a drastic improvement over the Challenge baseline (25.26 and 49.16 %). Further improvements can be obtained by system combination with a DRNN tandem recognizer, reaching 7.02 % and 19.61 % WER.
Staphylococcus aureus Bacteremia: Recurrence and the Impact of Antibiotic Treatment in a Prospective Multicenter Study

Staphylococcus aureus bacteremia is associated with substantial morbidity. Recurrence is common, but incidence and risk factors for recurrence are uncertain. The emergence of methicillin resistance and the ease of administering vancomycin, especially in patients who have renal insufficiency, have led to reliance on this drug with the assumption that it is as effective as β-lactam antibiotics, an assumption that remains open to debate.We initiated a multicenter, prospective observational study in 6 university hospitals and enrolled 505 consecutive patients with S. aureus bacteremia. All patients were monitored for 6 months and patients with endocarditis were followed for 3 years. Recurrence was defined as return of S. aureus bacteremia after documentation of negative blood cultures and/or clinical improvement after completing a course of antistaphylococcal antibiotic therapy. All blood isolates taken from patients with recurrent bacteremia underwent pulsed-field gel electrophoresis testing. Recurrence was subclassified as reinfection (different pulsed-field gel electrophoresis patterns) or relapse (same pulsed-field gel electrophoresis pattern). Forty-two patients experienced 56 episodes of recurrence (79% were relapses and 21% were reinfection). Relapse occurred earlier than reinfection (median, 36 versus 99 d, p < 0.06). Risk factors for relapse of S. aureus bacteremia included valvular heart disease, cirrhosis of the liver, and deep-seated infection (including endocarditis). Nafcillin was superior to vancomycin in preventing bacteriologic failure (persistent bacteremia or relapse) for methicillin-susceptible S. aureus (MSSA) bacteremia. Failure to remove infected intravascular devices/catheters and vancomycin therapy were common factors in patients experiencing multiple (greater than 2) relapses. However, by multivariate analysis, only endocarditis and therapy with vancomycin (versus nafcillin) were significantly associated with relapse.Recurrences occurred in 9.4% of S. aureus bacteremias following antistaphylococcal therapy, and most were relapses. Duration of antistaphylococcal therapy was not associated with relapse, but type of antibiotic therapy was. Nafcillin was superior to vancomycin in efficacy in patients with MSSA bacteremia.
TRANSCRIPTOME ANALYSES REVEAL DIFFERENTIAL GENE EXPRESSION PATTERNS BETWEEN THE LIFE‐CYCLE STAGES OF EMILIANIA HUXLEYI (HAPTOPHYTA) AND REFLECT SPECIALIZATION TO DIFFERENT ECOLOGICAL NICHES 1

Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life‐cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life‐cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life‐cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life‐cycle stages are capable of particle uptake (0.5 μm diameter) in late‐stationary growth phase. Results showed that the two life‐cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit.
Fruit consumption in migratory passerines is limited by water ingestion rather than by body water balance

Many insectivorous passerines become frugivorous during migration. Because water may facilitate the digestion of dry fruits, some passerines may benefit from staging in stopover sites that offer access to drinking water. In autumn, water consumption by blackcaps Sylvia atricapilla staging in Israel was found to induce a shift from insectivory to frugivory. We tested two alternative hypotheses concerning the mechanism facilitating consumption of the relatively dry fruits which are common in this region: 1) water intake facilitates the passage of fruits within the digestive tract when these two resources are simultaneously ingested, and 2) improved body water balance allows the consumption and ingestion of large amounts of dry fruits. Blackcaps were subjected to five treatments that included temporal separation of water and fruit consumption, as well as subcutaneous water injection to maintain balanced body water in water-deprived birds. Fruit consumption rate was measured daily. We found that only simultaneous provisioning of water and fruits significantly increased fruit consumption rate, implying that drinking water directly improves fruit digestion within the digestive system. Furthermore, the fuel deposition rate increased with increased fruit consumption rate. These results emphasize the importance of water availability for the ecology and conservation of migrating passerines.
Black holes as lumps of fluid

The old suggestive observation that black holes often resemble lumps of fluid has recently been taken beyond the level of an analogy to a precise duality. We investigate aspects of this duality, and in particular clarify the relation between area minimization of the fluid vs. area maximization of the black hole horizon, and the connection between surface tension and curvature of the fluid, and surface gravity of the black hole. We also argue that the Rayleigh-Plateau instability in a fluid tube is the holographic dual of the Gregory-Laflamme instability of a black string. Associated with this fluid instability there is a rich variety of phases of fluid solutions that we study in detail, including in particular the effects of rotation. We compare them against the known results for asymptotically flat black holes finding remarkable agreement. Furthermore, we use our fluid results to discuss the unknown features of the gravitational system. Finally, we make some observations that suggest that asymptotically flat black holes may admit a fluid description in the limit of large number of dimensions.
Evidence for Vasculoprotective Effects of ETB Receptors in Resistance Artery Remodeling in Diabetes

OBJECTIVE—Vascular remodeling, characterized by extracellular matrix deposition and increased media-to-lumen (M/l) ratio, contributes to the development of microvascular complications in diabetes. Matrix metalloproteinases (MMPs) play an important role in the regulation of extracellular matrix (ECM) turnover and vascular remodeling. Vasoactive factor endothelin (ET)-1 not only causes potent vasoconstriction but also exerts profibrotic and proliferative effects that change vessel architecture, which makes it a likely candidate for a key role in vascular complications of diabetes. Thus, this study investigated the regulation of MMP activity of resistance arteries under mild-to-moderate diabetes conditions, as seen in type 2 diabetes, and the relative role of ET receptors in this process. RESEARCH DESIGN AND METHODS—Vessel structure, MMP activity, and ECM proteins were assessed in control Wistar and diabetic Goto-Kakizaki (GK) rats treated with vehicle, ETA receptor antagonist atrasentan (5 mg · kg−1 · day−1), or ETB receptor antagonist A-192621 (15 mg · kg−1 · day−1) for 4 weeks. RESULTS—M/l ratio was increased in diabetes. Atrasentan prevented this increase, whereas A-192621 caused further thickening of the medial layer. Increased MMP-2 activity in diabetes was prevented by atrasentan treatment. Collagenase activity was significantly decreased in diabetes, and while ETA antagonism improved enzyme activity, ETB blockade further reduced collagenase levels. Accordingly, collagen deposition was augmented in GK rats, which was reversed by atrasentan but exacerbated with A-192621. CONCLUSIONS—ET-1 contributes to the remodeling of mesenteric resistance arteries in diabetes via activation of ETA receptors, and ETB receptors provide vasculoprotective effects.
Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge Aplysina aerophoba

ABSTRACT Marine sponges are natural sources of brominated organic compounds, including bromoindoles, bromophenols, and bromopyrroles, that may comprise up to 12% of the sponge dry weight. Aplysina aerophoba sponges harbor large numbers of bacteria that can amount to 40% of the biomass of the animal. We postulated that there might be mechanisms for microbially mediated degradation of these halogenated chemicals within the sponges. The capability of anaerobic microorganisms associated with the marine sponge to transform haloaromatic compounds was tested under different electron-accepting conditions (i.e., denitrifying, sulfidogenic, and methanogenic). We observed dehalogenation activity of sponge-associated microorganisms with various haloaromatics. 2-Bromo-, 3-bromo-, 4-bromo-, 2,6-dibromo-, and 2,4,6-tribromophenol, and 3,5-dibromo-4-hydroxybenzoate were reductively debrominated under methanogenic and sulfidogenic conditions with no activity observed in the presence of nitrate. Monochlorinated phenols were not transformed over a period of 1 year. Debromination of 2,4,6-tribromophenol, and 2,6-dibromophenol to 2-bromophenol was more rapid than the debromination of the monobrominated phenols. Ampicillin and chloramphenicol inhibited activity, suggesting that dehalogenation was mediated by bacteria. Characterization of the debrominating methanogenic consortia by using terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis analysis indicated that different 16S ribosomal DNA (rDNA) phylotypes were enriched on the different halogenated substrates. Sponge-associated microorganisms enriched on organobromine compounds had distinct 16S rDNA TRFLP patterns and were most closely related to the δ subgroup of the proteobacteria. The presence of homologous reductive dehalogenase gene motifs in the sponge-associated microorganisms suggested that reductive dehalogenation might be coupled to dehalorespiration.
Network analysis: a brief overview and tutorial

ABSTRACT Objective: The present paper presents a brief overview on network analysis as a statistical approach for health psychology researchers. Networks comprise graphical representations of the relationships (edges) between variables (nodes). Network analysis provides the capacity to estimate complex patterns of relationships and the network structure can be analysed to reveal core features of the network. This paper provides an overview of networks, how they can be visualised and analysed, and presents a simple example of how to conduct network analysis in R using data on the Theory Planned Behaviour (TPB). Method: Participants (n = 200) completed a TPB survey on regular exercise. The survey comprised items on attitudes, normative beliefs, perceived behavioural control, and intentions. Data were analysed to examine the network structure of the variables. The EBICglasso was applied to the partial correlation matrix. Results: The network structure reveals the variation in relationships between the items. The network split into three distinct communities of items. The affective attitude item was the central node in the network. However, replication of the network in larger samples to produce more stable and robust estimates of network indices is required. Conclusions: The reported network reveals that the affective attitudinal variable was the most important node in the network and therefore interventions could prioritise targeting changing the emotional responses to exercise. Network analysis offers the potential for insight into structural relations among core psychological processes to inform the health psychology science and practice.