Miracle-dz/UniFAR-FTUs huggingface dataset:
FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris

Purple non‐sulphur phototrophic bacteria (PNSB) are excellent models for analysing the co‐ordination of major metabolisms, including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In species studied to date, a two‐component system called RegBA controls these functions and it has been thought that this redox sensing regulatory system is essential for co‐ordinating electron flow and cannot be easily replaced. Here we show that this is not the case for all PNSB and that the oxygen‐sensing FixLJ‐K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and other major metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth. Transcriptome analyses indicated that FixK positively regulates haem and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for autotrophy and aromatic compound degradation. Purified FixK interacted with the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome‐histidine kinase gene and the fnr‐type regulatory gene, aadR. A FixK–AadR hierarchy mediates the transition from microaerobic to anaerobic growth. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms.
Type 1 Capsule Genes of Staphylococcus aureus Are Carried in a Staphylococcal Cassette Chromosome Genetic Element

ABSTRACT The cap1 genes are required for the synthesis of type 1 capsular polysaccharide (CP1) in Staphylococcus aureus. We previously showed that the cap1 locus was associated with a discrete genetic element in S. aureus M. In this report, we defined the boundaries of the cap1 element by comparing its restriction pattern to that of a corresponding region from the CP1-negative strain Becker. The element was located in the SmaI-G chromosomal fragment of the standard mapping strain NCTC8325. The sequences of the entire cap1 element and the flanking regions were determined. We found that there were two additional cap1 genes not previously identified. The cap1 operon was located in a staphylococcal cassette chromosome (SCC) element similar to the resistance island SCCmec recently described for methicillin resistance in S. aureus. Notably, the SCCcap1 element was located at the same insertion site as all the SCCmec elements in the staphylococcal chromosome. The excision of SCCcap1 could be demonstrated only in the presence of the recombinase genes from an SCCmec element, verifying that SCCcap1 is a genuine SCC element but defective in mobilization. A novel enterotoxin gene, whose transcript was detected by Northern blotting, was found next to the SCCcap1 locus. We propose that the enterotoxin gene and SCCcap1 were inserted into this locus at the juxtaposition by independent events. Sequence comparison revealed numerous DNA rearrangements and mutations in SCCcap1 and the left flanking region, suggesting that the SCCcap1 had been inserted at the SCC attC site a long time ago. In addition, most genes in this region were incomplete, with the exception of the 15 cap1 genes, implying that the cap1 genes confer a survival advantage on strain M.
High-Density Lipoprotein-Cholesterol, Daily Estradiol and Progesterone, and Mammographic Density Phenotypes in Premenopausal Women

High-density lipoprotein-cholesterol (HDL-C) may influence the proliferation of breast tumor cells, but it is unclear whether low HDL-C levels, alone or in combination with cyclic estrogen and progesterone, are associated with mammographic density, a strong predictor of breast cancer development. Fasting morning serum concentrations of HDL-C were assessed in 202 premenopausal women, 25 to 35 years of age, participating in the Norwegian Energy Balance and Breast Cancer Aspects (EBBA) I study. Estrogen and progesterone were measured both in serum, and daily in saliva, throughout an entire menstrual cycle. Absolute and percent mammographic density was assessed by a computer-assisted method (Madena), from digitized mammograms (days 7–12). Multivariable models were used to study the associations between HDL-C, estrogen and progesterone, and mammographic density phenotypes. We observed a positive association between HDL-C and percent mammographic density after adjustments (P = 0.030). When combining HDL-C, estradiol, and progesterone, we observed among women with low HDL-C (<1.39 mmol/L), a linear association between salivary 17β-estradiol, progesterone, and percent and absolute mammographic density. Furthermore, in women with low HDL-C, each one SD increase of salivary mid-menstrual 17β-estradiol was associated with an OR of 4.12 (95% confidence intervals; CI, 1.30–13.0) of having above-median percent (28.5%), and an OR of 2.5 (95% CI, 1.13–5.50) of having above-median absolute mammographic density (32.4 cm2). On the basis of plausible biologic mechanisms linking HDL-C to breast cancer development, our findings suggest a role of HDL-C, alone or in combination with estrogen, in breast cancer development. However, our small hypothesis generating study requires confirmation in larger studies. Cancer Prev Res; 8(6); 535–44. ©2015 AACR.
A noncoherent coded modulation for 16QAM

In this paper, we present a noncoherent coded 16QAM (NC-16QAM) scheme by modifying the trellis-coded 16QAM (TC-16QAM) scheme. The simulation results show that the performance of the NC-16QAM with noncoherent detection is close to the one of the original TC-16QAM with coherent detection. The NC-16QAM in this paper is an extension of the NC-8PSK recently obtained by Wei and Lin (see IEEE Communications Letters, vol.2, no.9, p.260-2, Sept. 1998). A noncoherent initial phase estimation algorithm is also proposed.
The Effect of Maternal Weight Gain in Pregnancy on Birth Weight

The association between maternal weight gain during pregnancy and the infant's birth weight was studied in 14,121 term singleton births. The parturients were stratified into four body-mass categories, three age groups, four parity groups, and three levels of educational attainment. A separate multiple regression analysis was performed for each category to control for the confounding effect of gestational age, maternal social class, ethnicity, cigarette consumption, marital status, age, parity, education, and weight for height. A significant positive influence of prenatal weight gain on birth weight was found for all subgroups. The effect varied depending on maternal pre-pregnancy body mass, age, parity, and the level of formal education. (Obstet Gynecol 74:240, 1989)
Prediction of complicated grief by positive and negative themes in narratives.

A narrative coding system was employed to investigate the thematic parameters of complicated grief among participants who had recently experienced spousal loss. Two goals guided the research. First, we investigated the prevalence of and interrelationship between positive and negative themes in a narrative interview conducted 6 months into bereavement. The coding system was modeled after Erikson's (1982) scheme of crises solutions across the life span. Second, we examined the relationship of these themes to various symptom measures obtained at 6- and 14 months postloss. Results revealed no systematic relationship between corresponding positive and negative themes. Aggregated positive and negative themes showed significant correlations with 6-month measures of intrusion and avoidance and, as predicted, with various 14-month symptom levels. Regression analyses revealed that positive themes explained significant portions of 14-month symptom variance, even when 6-month symptom scores were controlled. Findings are discussed with regard to conceptualizations of grief as a stress response syndrome, where intrusive processes (e.g., in narration) are of importance.
The anatomy of osteoarthritic joint pain

The anatomical understanding of the pain generators in osteoarthritis (OA) is incomplete and the teaching about these pain generators in medical school anatomy/histology courses is minimal. This review covers the nociceptive innervation of synovial joints for the purposes of teaching. Studies that discuss the presence of neuropeptides involved in pain, such as Substance P (SP) and calcitonin‐gene‐related peptide, are the focus of this review. Nociceptive free‐nerve endings and SP staining nerves are found in the accessory ligaments, synovium, subchondral bone, menisci, and periosteum. The vasculature may also play a role in pain generation through vasospasm or ischemia, but this has yet to be proven. Joint denervation may relieve joint pain showing that it is indeed articular nerves that are carrying pain impulses but denervation does not identify the precise source of the pain. It remains unclear which of the anatomical loci of pain generation are primary in OA and if sources of pain vary in different patients and in different joints. Clin. Anat. 27:451–454, 2014. © 2012 Wiley Periodicals, Inc.
Using Dynamic Programming For Minimizing The Energy Of Active Contours In The Presence Of Hard Constraints

Energy-Minimizing Active Contour Models (snakes) have recently been proposed by Kass et al. [8] as a top-down mechanism for locating features of interest in images. The Kass et al.’s algorithm involves four steps: setting up a variational integral on the continuous plane, deriving a pair of Euler equations, discretizing them, and solving the discrete equations iteratively until convergence. This algorithm suffers from a number of problems. We discuss these problems and present an algoIithm for active contours based on dynamic programming. The optimization problem is set up as a discrete multi-stage decision process and is solved by a “time-delayed” discrete dynamic programming algorithm. This formulation leads to a stable behavior for the active contours over iterations, in addition to allowing for hard constraints to be enforced on the behavior of the solution. Results of the application of the proposed algorithm to real images is presented.
The Epidemiology of Glenohumeral Joint Instability: Incidence, Burden, and Long-term Consequences

Acute traumatic glenohumeral joint instability is common within the general population and endemic in young athletes and physically active populations. Individuals who experience acute traumatic glenohumeral joint instability events are at high risk of recurrent injury. In addition, glenohumeral joint instability results in substantial short-term and long-term consequences, including significant time loss from activity, degenerative joint changes, and reduced quality of life. This review provides an overview of the epidemiology of glenohumeral joint instability, reviews the modifiable and nonmodifiable risk factors for glenohumeral joint instability identified in the literature, and discusses the need for developing and implementing effective multilevel strategies for the primary, secondary, and tertiary prevention of glenohumeral joint instability and the long-term consequences associated with injury.
Antibacterial activity of aqueous and methanol extracts of selected species used in livestock health management

Abstract Context: Salvadora persica L. (Salvadoraceae), Colophospermum mopane (J.Kirk ex Benth.) J. Léonard (Leguminosae) and Dichrostachys cinerea (L.) Wight & Arn. (Leguminosae) crude extracts are used by local farmers against many livestock infections with little or no side effects usually associated with synthetic antimicrobials. However, their efficacy has rarely been tested. Objective: These plants were tested for potential antibacterial activity against clinical isolates of Staphylococcus aureus ATCC33862 and Escherichia coli ATCC25922. Minimal inhibitory concentrations (MIC) of the crude plant extracts were determined. Materials and methods: Aqueous and methanol extraction of 100 g each of the bark of C. mopane, roots of D. cinerea and leaves of S. persica was done by placing the samples in 250 mL of either water or methanol. Nutrient broth was used as growth medium for the bacteria, and McFarland standard for bacterial standardization. 2,3,5-Triphenyltetrazoliumchloride (TTC) was the indicator salt. Each of the aqueous and methanol extracts (100 μL) was tested. Gentamycin and ampicillin were the controls. Results: MIC of aqueous extracts ranged from 1.03–14.6 mg/mL against S. aureus, and from 12.1–34.3 mg/mL against E. coli. Methanol extracts ranged between 5.31 and 9.64 mg/mL against S. aureus, and between 7.86 and 13.6 mg/mL against E. coli. Aqueous and methanol extracts of S. persica were significantly higher (p < 0.05) than C. mopane and D. cinerea. Discussion and conclusion: Colophospermum mopane, S. persica and D. cinerea exhibited antibacterial activity, with methanol extracts performing better than aqueous extracts, justifying use as ethnoveterinary medicine. Further study to isolate the active components should be pursued.
Limit and organization of the cortical projection from the medial thalamic nucleus in monkey

The projection of n. medialis dorsalis on the anterior part of the frontal cortex of primates is established, but evidence concerning extent and internal arrangement of this nuclear projection provides an insufficient guide to finer cortical par­ cellation. In the course of experiments designed primarily to investigate the effects on behavior of partial frontal ab­ lation, we have analyzed retrograde thalamic degeneration in 40 cerebral hemispheres of Macaca mulatta. Our results, sup­ plemented by those of other investigators, indicate the to­ pology of thalamo-cortical correspondence. On the basis of its cellular appearance, 'Walker ('38, '40) divides the nucleus into a lateral paralamellar part, an an­ teromedial magllOcellular part, and a main parvicellular part. He assigns the projection of the paralamellar'and lateral par­ vicellular portions to the cortex anterior to the arcuate sul­ cus; the magnocellular and medial parvicellular parts to the orbital surface. He finds that the par'alamellar division pro­ jects more posteriorly than the lateral parvicellular part, but he is unable to differentiate between magnocellular and me1 Present address, Research Laboratories, Institute of Living, Hartford, Con­ necticut.
Optimization of multiplex PCR conditions for rapid detection of Escherichia coli O157:H7 virulence genes.

The main source of E. coli 0157:H7 is cattle, but recent studies showed high percentage of outbreaks contributed by contaminated water. The occurrence of E. coli O157:H7 in environmental water samples poses a potential threat to human health. The aim of this study was to establish a protocol for the detection of the pathogen E. coli O157:H7 and E. coli virulence genes (eaeA, rfbE, hly, stx 1, and stx 2) in a multiplex PCR protocol using six specific primer pairs. The target genes produced species-specific amplicons at 625 bp, 397 bp, 296 bp, 166 bp, 210 bp and 484 bp for E. coli O157:H7 (fliC h7 gene) and virulence genes (eaeA, rfbE, hly, stx 1, and stx 2) respectively. The results obtained show that the established PCR protocol is suitable for a rapid and specific analysis of the pathogenic E. coli O157:H7 in environmental water samples for the assessment of microbiological risks.
Transient Umbilical Cord Occlusion in Late-Gestation Fetal Sheep Results in Hippocampal Damage but Not in Cerebral Arteriovenous Difference for Nitrite, a Stable End Product of Nitric Oxide

Objective: To investigate the effect of total umbilical cord occlusion on cerebral arteriovenous difference for nitrite (a stable end product of nitric oxide) and neuronal outcome. Method: The cord was totally occluded for 10 minutes in 14 late-gestation (gestational age 113-120 days) chronically instrumented fetal sheep. Arterial (carotid artery) and venous (superior sagittal sinus) blood samples were taken at regular intervals for determination of acid-base status, glucose, lactate, and nitrite plasma levels. Three days after the occlusion period the fetal brain was perfusion fixed, and the parietal cortex, hippocampus, and cerebellum were scored for neuronal damage. Results: Three fetuses died shortly after the occlusion period. Total umbilical cord occlusion resulted in a combined respiratory and metabolic acidosis as observed in carotid arterial blood gas samples (pH, 6.96 ± 0.02; CaO2 [mmol/L], 0.43 ± 0.9; Paco2 [kPa], 13.46 ± 0.38; base excess [mmol/L], -11.1 ± 0.8; lactate [mmol/L], 10.57 ± 0.95; bradycardia, 75 ± 9 bpm; and hypotension, 29.85 ± 3.00 mmHg) (n = 14, values are mean ± standard error of the mean). Selective brain damage was observed in the hippocampus in 10 of the 11 surviving fetal sheep. No changes in arterial, venous, or cerebral arteriovenous difference for nitrite plasma levels were observed (n = 11). Conclusion: Total umbilical cord occlusion of 10 minutes in preterm fetal sheep results in hippocampal damage but not in changes of cerebral arteriovenous difference for nitrite plasma levels, a stable end product of nitric oxide.
Rapid Drug Tolerance and Dramatic Sterilizing Effect of Moxifloxacin Monotherapy in a Novel Hollow-Fiber Model of Intracellular Mycobacterium kansasii Disease

ABSTRACT Mycobacterium kansasii is the second most common mycobacterial cause of lung disease. Standard treatment consists of rifampin, isoniazid, and ethambutol for at least 12 months after negative sputum. Thus, shorter-duration therapies are needed. Moxifloxacin has good MICs for M. kansasii. However, good preclinical models to identify optimal doses currently are lacking. We developed a novel hollow fiber system model of intracellular M. kansasii infection. We indexed the efficacy of the standard combination regimen, which was a kill rate of −0.08 ± 0.05 log10 CFU/ml/day (r2 = 0.99). We next performed moxifloxacin dose-effect and dose-scheduling studies at a half-life of 11.1 ± 6.47 h. Some systems also were treated with the efflux pump inhibitor reserpine. The highest moxifloxacin exposure, as well as lower exposures plus reserpine, sterilized the cultures by day 7. This suggests that efflux pump-mediated tolerance at low ratios of the area under the concentration-time curve from 0 to 24 h (AUC0–24) to MICs is an early bacterial defense mechanism but is overcome by higher exposures. The highest rate of moxifloxacin monotherapy sterilization was −0.82 ± 0.15 log10 CFU/ml/day (r2 = 0.97). The moxifloxacin exposure associated with 80% of maximal kill (EC80) was an AUC0–24/MIC of 317 (the non-protein-bound moxifloxacin AUC0–24/MIC was 158.5). We performed Monte Carlo simulations of 10,000 patients in order to identify the moxifloxacin dose that would achieve or exceed the EC80. The simulations revealed an optimal moxifloxacin dose of 800 mg a day. The MIC susceptibility breakpoint at this dose was 0.25 mg/liter. Thus, moxifloxacin, at high enough doses, is suitable to study in patients for the potential to add rapid sterilization to the standard regimen.
Resilience as Adaptation in Older Women

ABSTRACT This article discusses factors that contribute to resilience in older women. Face-to-face audio taped interviews with seventeen women between the ages of seventy and eighty were the primary data source. Open-ended questions related to the experience of advantage and adversity across the life span comprised the interview guide. Paths to resilience were variously affected depending on developmental, social-structural, historical, and individual life story influences. Among seven factors that emerged as salient to resilience in the sample are the external resource of social connectedness and internal resources, including a “head-on” approach to challenge and spiritual grounding. Pivotal in the women's lives were curiosity and extending self to others. Moving forward with life following adversity and “maverick” (nontraditional) behavior facilitated preservation of the self in these resilient women.
Analysis of the doubler of electricity considering a resistive load

This work shows a detailed analysis of an electrostatic generator based on Bennet's doubler, that can be used for vibrational energy harvesting, considering the effect of a resistive load on the behavior of the device. Two levels of approximation are used in the analysis, with results compared with precise simulations. The analyses allow a prediction of the voltage multiplication factor per cycle as function of the load, and quick evaluation of the load that the device can tolerate.
Spiral Fractures and Bone Pseudotools at Paleontological Sites

Spiral ("green bone") breakage has been suggested as an indicator of human activity by some workers. Our examination of broken ungulate long bones from six paleontological localities in western Nebraska, however, shows that such fractures commonly occurred in the Miocene and Pliocene, long before the advent of man in North America. Pseudotools also occur frequently in these sites. We postulate that spiral breakage, including the production of pseudotools, may be due to trampling by animals. Our study demonstrates that neither spiral breakage nor gross morphology, alone or in combination, is diagnostic of human activity. Problematical examples must be accepted or rejected wholly upon the basis of patterned wear on the supposed tools.
Double-guidewire technique in difficult biliary cannulation for the prevention of post-ERCP pancreatitis: a systematic review and meta-analysis

Abstract Background and study aims Difficult cannulation is a risk factor for pancreatitis following endoscopic retrograde cholangiopancreatography (ERCP). The double-guidewire technique (DGT) may improve cannulation success and reduce the risk of post-ERCP pancreatitis (PEP) in patients with difficult cannulation. This systematic review compared the DGT with persistent conventional cannulation or other advanced techniques in patients with difficult cannulation. Patients and Methods CENTRAL, MEDLINE, EMBASE, and CINAHL databases and DDW and UEGW abstracts up to March 2016 were searched for randomized controlled trials (RCTs) comparing DGT with persistent conventional cannulation or other advanced techniques (precut, pancreatic duct [PD] stenting). The primary outcome was PEP. Secondary outcomes included severity of PEP, successful cannulation of the common bile duct (CBD) with the randomized technique, overall CBD cannulation success, and ERCP-related complications. Results 7 RCTs (577 patients) were included. Use of the DGT significantly increased PEP compared to other endoscopic techniques (risk ratio [RR] 1.98, 95 % confidence interval [95 %CI] 1.14 – 3.42). There was no significant difference in CBD cannulation success with the randomized technique (RR 1.04, 95 %CI 0.87 – 1.24) or in overall cannulation success (RR 1.04, 95 %CI 0.91 – 1.18) between DGT and other techniques. There was also no significant difference in the risk of other ERCP-related complications (bleeding, perforation, cholangitis, and mortality). The results were robust in sensitivity analyses. Conclusions In patients with difficult cannulation, sole use of the DGT appears to increase the risk of PEP without any superiority in achieving biliary cannulation compared to other techniques. PD stenting may reduce the risk of PEP when the DGT is used. The influence of co-intervention in the form of per-procedural nonsteroidal anti-inflammatory drug (NSAID) administration is unclear.