Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian rhythms of superhelical status of DNA in cyanobacteria

The cyanobacterium Synechococcus elongatus expresses robust circadian (daily) rhythms under the control of the KaiABC-based core clockwork. Unlike eukaryotic circadian systems characterized thus far, the cyanobacterial clockwork modulates gene expression patterns globally and specific clock gene promoters are not necessary in mediating the circadian feedback loop. The oscilloid model postulates that global rhythms of transcription are based on rhythmic changes in the status of the cyanobacterial chromosome that are ultimately controlled by the KaiABC oscillator. By using a nonessential, cryptic plasmid (pANS) as a reporter of the superhelical state of DNA in cyanobacteria, we show that the supercoiling status of this plasmid changes in a circadian manner in vivo. The rhythm of topological change in the plasmid is conditional; this change is rhythmic in constant light and in light/dark cycles, but not in constant darkness. In further support of the oscilloid model, cyanobacterial promoters that are removed from their native chromosomal locations and placed on a plasmid preserve their circadian expression patterns.
Clinical and economic outcomes associated with amlodipine/renin–angiotensin system blocker combinations

Objectives: Since treatment regimen type can influence adherence and other outcomes, this study examined adherence, cardiovascular events, and economic outcomes in patients with hypertension treated with fixed-dose combination (FDC) amlodipine/olmesartan (AML/OM), FDC AML/benazepril (AML/BEN), and loose-dose combination AML plus angiotensin II receptor blockers (LDC AML/ARBs). Methods: Commercial health plan enrolees aged at least 18 years with index claim(s) for AML/OM, AML/BEN, or LDC AML/ARB were identified. Absence of study drug 6 months pre index, and continuous enrolment for at least 12 months post index were required. Descriptive analyses were executed to make comparisons between treatments, as well as multivariate models adjusting for baseline demographic and clinical characteristics, including propensity for assignment to study drug. Results: Descriptive results suggested mean follow-up adherence was higher in the AML/OM cohort [proportion of days covered (PDC) = 0.63] compared with the AML/BEN (PDC = 0.55; p < 0.001) and LDC AML/ARB cohorts (PDC = 0.34; p < 0.001). The proportion of individuals with an incident follow-up cardiovascular event composite was lower in the AML/OM cohort versus the AML/BEN and LDC AML/ARB cohorts (5.94% versus 7.85% and 16.89% respectively). Adjusted Cox models suggested that patients initiated on LDC AML/ARB (hazard ratio 1.35; p < 0.001), but not on AML/BEN, were at greater risk of a follow-up cardiovascular event (composite) compared with AML/OM. Adjusted generalized linear models suggested that mean follow-up per-member-per-month overall costs were higher in the AML/BEN (cost ratio = 1.169; p < 0.001; unadjusted mean cost US$780) and LDC AML/ARB cohorts (cost ratio = 1.286; p < 0.001; unadjusted mean cost US$1394) compared with the AML/OM cohort (unadjusted mean cost US$740). Conclusion: The results suggested that treatment with FDC AML/OM was associated with greater likelihood of adherence and lower overall costs than with FDC AML/BEN and LDC AML/ARB, and lower risk of cardiovascular event composite versus LDC AML/ARB.
Neuromuscular Performance of Elite Rugby Union Players and Relationships With Salivary Hormones

Crewther, BT, Lowe, T, Weatherby, RP, Gill, N, and Keogh, J. Neuromuscular performance of elite rugby union players and relationships with salivary hormones. J Strength Cond Res 23(7): 2046-2053, 2009-This study compared the neuromuscular performance (speed, power, strength) of elite rugby union players, by position, and examined the relationship between player performance and salivary hormones, by squad and position. Thirty-four professional male rugby players were assessed for running speed (10-m, 20-m or 30-m sprints), concentric mean (MP) and peak power (PP) during a 70-kg squat jump (SJ) and 50-kg bench press throw (BT), and estimated 1 repetition maximum (1RM) strength for a box squat (BS) and bench press (BP). Tests were performed on separate days with absolute and normalized (power and strength only) values computed. Saliva was collected before each test and assayed for testosterone (Sal-T) and cortisol (Sal-C). In absolute terms, the backs demonstrated greater speed and BT MP, whereas the forwards produced greater SJ PP and MP and BS 1RM (p < 0.01). However, BT, SJ and BS performances were no different when normalized for body mass in kg0.67 (p > 0.05). A comparison (absolute and normalized) of BT PP showed no positional differences (p > 0.05), whereas BP 1RM was greater for the forwards (p < 0.05). These results may be attributed to genetic and/or training factors relating to the positional demands of rugby. The Sal-T and/or Sal-C concentrations of players correlated to speed, power, and strength, especially for the backs (p < 0.05), thereby confirming relationships between neuromuscular performance and hormone secretion patterns. Based on these findings, it was suggested that training to increase whole-body and muscle mass might facilitate general performance improvements. Training prescription might also benefit from acute and chronic hormone monitoring to identify those individuals likely to respond more to hormonal change.
Muscle Organization in Individuals with and without Pain and Joint Dysfunction

Central nervous system organization of masticatory muscles determines the magnitude of joint and muscle forces. Validated computer-assisted models of neuromuscular organization during biting were used to determine organization in individuals with and without temporomandibular disorders (TMD). Ninety-one individuals (47 women, 44 men) were assigned to one of four diagnostic groups based on the presence (+) or absence (-) of pain (P) and bilateral temporomandibular joint disc displacement (DD). Electromyography and bite-forces were measured during right and left incisor and molar biting. Two three-dimensional models employing neuromuscular objectives of minimization of joint loads (MJL) or muscle effort (MME) simulated biting tasks. Evaluations of diagnostic group and gender effects on choice of best-fit model were by analysis of variance (ANOVA) and Tukey-Kramer post hoc tests, evaluations of right-left symmetry were by Chi-square and Fisher’s exact statistics, and evaluations of model accuracy were by within-subject linear regressions. MME was the best-fit during left molar biting in +DD individuals and incisor biting in men (all p < 0.03). Incisor biting symmetry in muscle organization was significantly higher (p < 0.03) in healthy individuals compared with those with TMD. Within-subject regressions showed that best-fit model errors were similar among groups: 8 to 15% (0.68 ≤ R2 ≤ 0.74). These computer-assisted models predicted muscle organization during static biting in humans with and without TMDs.
Visualizing Science by Citation Mapping

Science mapping is discussed in the general context of information visualization. Attempts to construct maps of science using citation data are reviewed, focusing on the use of co-citation clusters. New work is reported on a dataset of about 36,000 documents using simplified methods for ordination, and nesting maps hierarchically. An overall map of the dataset shows the multidisciplinary breadth of the document sample, and submaps allow drilling down to the document level. An effort to visualize these data using advanced virtual reality software is described, and the creation of document pathways through the map is seen as a realization of Bush's (1945) associative trails.
Morphology of deltoid origin and end tendons – a generic model

This study provides a model of the complex deltoid origin and end tendons, as a basis for further anatomical, biomechanical and clinical research. Although the deltoid is used in transpositions with upper limb paralysis, its detailed morphology and segmentation has not been object of much study. Morphologically, the deltoid faces two distinct challenges. It closely envelops a ball joint, and it reduces its width over a short distance from a very wide origin along clavicle, acromion and spina scapula, to an insertion as narrow as the humerus. These challenges necessitate specific morphological tendon adaptations. A qualitative model for these tendons is developed by the stepwise transformation of a unipennate muscle model into a functional deltoid muscle. Each step is the solution to one of the mentioned morphological challenges. The final model is of an end tendon consisting of a continuous succession of bipennate end tendon blades centrally interspaced by unipennate tendon parts. The origin tendon consists of lamellae that interdigitate with the end tendon blades, creating a natural segmentation. The model is illustrated by qualitative dissection results. In addition, in view of a proliferation of terms found in the literature to describe deltoid tendons, tendon concepts are reviewed and the systematic use of the unique and simple terminology of ‘origin and end tendons’ is proposed.
Ascosphaera subglobosa, a new spore cyst fungus from North America associated with the solitary bee Megachile rotundata

Ascosphaera subglobosa (Eurotiomycetes: Onygenales) is newly described from the pollen provisions and nesting material of the solitary leaf-cutting bee Megachile rotundata in Canada and the western United States. This new species, related to A. atra and A. duoformis, is distinguished from other Ascosphaera species by its globose to subglobose ascospores, evanescent spore balls and unique nuclear ribosomal DNA sequences (ITS and LSU).
Epidemiology of Bloodstream Candida spp. Infections Observed During a Surveillance Study Conducted in Spain

Candida bloodstream infections (BSI) have become a major healthcare problem, specially in tertiarycare hospitals worldwide (Al-Jasser & Elkhizzi, 2004, Almirante et al., 2005, AlonsoValle et al., 2003, Atunes et al., 2004 Asmundsdottir et al., 2002, Costa et al., 2000, Fraser et al., 1992, Garbino et al., 2002, Luzzati et al. 2000, Marchetti et al., 2004, Pappas et al., 2003, Viudes et al., 2002). Several risk factor identified among patients hospitalized for long periods such as the exposition to broad spectrum antimicrobial and/or immunosuppressive chemotherapy, parenteral nutrition, and invasive medical procedures have contributed to this fact (Blumberg et al., 2001, Fraser et al., 1992). Despite some improvements in fungal BSI diagnosis during last years, candidemia diagnosis remains difficult. Besides, following the data appeared in the classical study from Berenguer and colleagues, only 50% of patients with disseminated candidiasis will have positive blood cultures and even fewer will have an antemortem diagnosis (15% to 40%) (Berenguer et al., 1993). Therefore, invasive candidemia is not easy to diagnose, has an expensive treatment and finally is a serious, often lifethreatening infection (Girmenia et al., 1996, Messer et al., 2009).
Effect of timing of food deprivation on host resistance to fungal infection in mice

Mice were deprived of food for a period of 72h at varying times relative to the time of infection with Paracoccidioides brasiliensis. Host resistance was diminished profoundly when the period of food deprivation was from 48h before to 24h after infection (group B). When food deprivation was initiated immediately after infection (group C), host resistance was reduced less profoundly. When food deprivation was initiated at 24 and 48h post-infection, reductions in host resistance were only moderate or not observed respectively. These results suggest that the earlier in the course of infection starvation occurs, the more profoundly host resistance is impaired. When food deprivation was initiated 72h before infection, finishing at the time of infection (group A), the reduction in host resistance was considerably less profound compared with group B mice, suggesting that refeeding initiated immediately after infection is responsible for rapid restoration of the antifungal resistance in starved mice. Infection-induced responses of corticosterone and interferon-γ were changed according to the timing of food deprivation. Group A mice, similar to non-fasted controls, showed an infection-induced increase in serum corticosterone concentration, while groups B and C did not. Group C mice showed a substantially greater infection-induced increase in serum interferon-γ compared with the other fasted and non-fasted control groups.
Xtalk: a path-based approach for identifying crosstalk between signaling pathways

MOTIVATION Cells communicate with their environment via signal transduction pathways. On occasion, the activation of one pathway can produce an effect downstream of another pathway, a phenomenon known as crosstalk. Existing computational methods to discover such pathway pairs rely on simple overlap statistics. RESULTS We present Xtalk, a path-based approach for identifying pairs of pathways that may crosstalk. Xtalk computes the statistical significance of the average length of multiple short paths that connect receptors in one pathway to the transcription factors in another. By design, Xtalk reports the precise interactions and mechanisms that support the identified crosstalk. We applied Xtalk to signaling pathways in the KEGG and NCI-PID databases. We manually curated a gold standard set of 132 crosstalking pathway pairs and a set of 140 pairs that did not crosstalk, for which Xtalk achieved an area under the receiver operator characteristic curve of 0.65, a 12% improvement over the closest competing approach. The area under the receiver operator characteristic curve varied with the pathway, suggesting that crosstalk should be evaluated on a pathway-by-pathway level. We also analyzed an extended set of 658 pathway pairs in KEGG and to a set of more than 7000 pathway pairs in NCI-PID. For the top-ranking pairs, we found substantial support in the literature (81% for KEGG and 78% for NCI-PID). We provide examples of networks computed by Xtalk that accurately recovered known mechanisms of crosstalk. AVAILABILITY AND IMPLEMENTATION The XTALK software is available at http://bioinformatics.cs.vt.edu/~murali/software. Crosstalk networks are available at http://graphspace.org/graphs? tags=2015-bioinformatics-xtalk. CONTACT ategge@vt.edu, murali@cs.vt.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Factors affecting falls in community-dwelling individuals with stroke in Singapore after hospital discharge.

INTRODUCTION This study aimed to investigate the factors affecting the incidence of falls among individuals with stroke living in the community one year after discharge from a rehabilitation hospital in Singapore. METHODS A cross-sectional telephone survey of individuals with stroke living in the community was carried out one year after discharge. The interview covered aspects such as incidence and circumstances of fall, use of walking aids, and presence of environmental obstacles. Each participant's case record was retrospectively reviewed using discharge Fugl-Meyer (FM) assessment of the upper and lower limbs, functional independence measure (FIM) and Berg Balance Scale (BBS). RESULTS A total of 126 individuals with stroke were interviewed. Overall, 24% fell in the year following their discharge. Factors associated with falls were longer length of hospital stay, lower BBS and lower-limb FM scores, and lower discharge FIM scores for the Bladder and Bowel Management, Transfer, Mobility, Communication, and Social Cognition domains (p < 0.05). The fallers were more likely to use walking aids, and required help with basic activities of daily living after discharge (p < 0.05). Multivariate logistic regression analysis revealed that only the Transfer domain was an independent factor for falls. CONCLUSION Discharge FIM outcomes, especially for the Transfer domain, can be used to identify communitydwelling individuals with stroke who have a high fall risk after discharge. Identification of such individuals will enable early fall prevention management, which will in turn minimise fall events in the community.
Alternative sugar beet production using shallow tillage and municipal solid waste fertiliser

The application of conventional agricultural practices, e.g. deep soil tillage and repeated, plentiful mineral fertilisation, can lead to a progressive deterioration of soil fertility, especially in Mediterranean environments characterised by scanty rains and high summer temperatures. As a consequence, to maintain high levels of both crop productivity and soil organic matter and to improve some soil properties, a reduction of agricultural inputs and a greater supply of organic material are needed. In the light of these considerations, we carried out a two-year field experiment in Southern Italy to determine the effects of reduced soil tillage and municipal solid waste compost application on growth parameters, production and quality of sugar beet crops, and on both soil chemical characteristics and mineral nitrogen deficit. Two soil tillage depths were compared: conventional tillage, till 40–45 cm and shallow tillage, at 15–20 cm. Within each soil tillage, the following N-fertilising strategies were tested: (1) mineral fertilisation, with 100 kg N ha−1; (2) organic fertilisation with municipal solid waste compost at 100 kg N ha−1; (3) mixed fertilisation, with 50% of organic N as municipal solid waste compost, and 50% of mineral N; and (4) slow-release organic-mineral N fertiliser, at 100 kg N ha−1. All these treatments were compared with a lower level of mineral fertiliser at 50 kg N ha−1, and with an unfertilised control. Our findings show first the absence of a significant difference in root and sucrose yields between reduced tillage and deep tillage; as shown by roots (36.02 t ha−1) and sucrose (3.41 t ha−1) yields for reduced tillage and 35.76 and 3.51 t ha−1, respectively, for the deepest tillage. Secondly, among the N treatments, the mixed organic-mineral N fertilisation gave productions statistically not different from mineral N fertilisation; as shown by root yields (36.38 versus 36.40 t ha−1) and sucrose yields (3.56 versus 3.65 t ha−1). Third, the mixed organic-mineral N induced a reduction of 13.2% in α-amino N content by comparison with the mineral treatment of 100 kg N ha−1. Fourth, our results showed that the applications of the municipal solid waste compost increased the extracted and the humified organic carbon by +27.7 and +25.4%, compared with the mineral fertiliser, and did not raise the content of heavy metals. These findings highlighted that in Southern Italy it is sustainable to adopt alternative sugar beet production, safeguarding crops’ quantitative and qualitative performance, decreasing the production costs and using the natural resources better.
Postoperative pain experiences in Chinese adult patients after thoracotomy and video‐assisted thoracic surgery

AIMS AND OBJECTIVES To investigate the developing course of postoperative pain in a Chinese sample of patients following thoracic surgery. BACKGROUND Chronic postoperative pain following thoracic surgery including both thoracotomy and video-assisted thoracic surgery is often reported. However, research on pain trends concerning this topic is scarce with a notable lack of culturally focused studies by nurses. DESIGN A prospective observational study. METHODS The sample included patients undergoing thoracotomy (n = 137) and video-assisted thoracic surgery (n = 143). Pain intensity and interference of pain with function were assessed during hospitalisation (day 1 to day 7 postoperatively) and followed up by telephone at 2 weeks and then at 1, 2, 3 and 6 months after surgery. RESULTS Moderate-to-severe pain when coughing and moving was reported in over 85% during hospitalisation, and a significant difference in pain was found between those undergoing a thoracotomy (61%) and those having video-assisted surgery (34%). Many patients whose immediate postoperative pain was poorly managed tended to report high pain levels after discharge and continued to have clinically important chronic pain 6 months after surgery. The pain intensity mean score during movement in the first five postoperative days was an important predictor of clinically important chronic pain, and those experiencing severe acute pain during hospitalisation had a higher probability of developing chronic pain. CONCLUSIONS Postoperative pain after thoracic surgery warrants greater attention because those experiencing severe acute pain during hospitalisation have a higher probability of developing chronic pain. Aggressive pain management and multimodal analgesia are recommended to prevent long-term suffering in patients. RELEVANCE TO CLINICAL PRACTICE Chronic pain after thoracic surgery remains a challenge in clinical nursing. To improve pain management quality and to prevent the transition of acute postoperative pain to chronic pain, standardised practice protocols and comprehensive physician and nurse education are highly recommended.
Neural correlates of movement generation in the ‘at‐risk mental state’

Broome MR, Matthiasson P, Fusar‐Poli P, Woolley JB, Johns LC, Tabraham P, Bramon E, Valmaggia L, Williams SCR, Brammer MJ, Chitnis X, McGuire PK. Neural correlates of movement generation in the ‘at‐risk mental state’.
Clinical and morphologic features of hypertrophic cardiomyopathy in elderly patients 85 years or older.

We studied the distinctive morphology of the left ventricle (LV) and attempted to relate advanced age and hypertension to this characteristic feature in elderly patients with hypertrophic cardiomyopathy (HC). Fourteen elderly patients > or = 85 years old (mean age 90 +/- 5 years) with HC were compared with 45 young patients < or = 40 years (mean age 34 +/- 4 years) with this disease. More mild hypertension in the elderly (10/14, 71%) than in the young (0%), and more syncope in the young (10/45, 22%) than in the elderly (0%) were observed. Echocardiography showed that the elderly patients had relatively mild LV wall thickening, generally confined to the septum (elderly vs young: 18 +/- 4 vs 25 +/- 8 mm, p < 0.001), with more basal septal bulging (elderly vs young: 12/14, 86% vs 0%, p < 0.001) and anterior septal hypertrophy of LV (elderly vs young: 11/14, 79% vs 0%, p < 0.001). Elderly patients with mild hypertension showed a predominantly basal septal bulging (10/10, 100%) and anterior septal hypertrophy of LV (9/10, 90%). HC in elderly patients > or = 85 years old has a striking LV morphology. Mild hypertension and advanced age may contribute to the distinctive geometry.
Neighbourhood SAC for Constraint Satisfaction Problems with Non-Binary Constraints

Neighbourhood singleton arc consistency (NSAC) is a type of singleton arc consistency (SAC) in which the subproblem formed by variables adjacent to a variable with a singleton domain is made arc consistent. In this paper we consider how to apply this form of consistency reasoning to problems with n - ary constraints including global constraints. The chief problem encountered is that of neighbouring variables contained in a constraint that also includes non-neighbouring variables. In this case, a strict extension of NSAC involves projection of such constraints onto the neighbourhood variables, but for many global constraints this may be difﬁcult to do in practice. Here, we consider a simple variant called restricted neighbourhood SAC, that avoids this problem. We compare the two approaches on random and structured problems and show that in all cases the restricted form of k -NSAC is nearly as effective as the unrestricted form.