Miracle-dz/UniFAR-FTUs huggingface dataset:
Methodological accuracy of image‐based electron density assessment using dual‐energy computed tomography

Purpose Electron density is the most important tissue property influencing photon and ion dose distributions in radiotherapy patients. Dual‐energy computed tomography (DECT) enables the determination of electron density by combining the information on photon attenuation obtained at two different effective x‐ray energy spectra. Most algorithms suggested so far use the CT numbers provided after image reconstruction as input parameters, i.e., are imaged‐based. To explore the accuracy that can be achieved with these approaches, we quantify the intrinsic methodological and calibration uncertainty of the seemingly simplest approach. Methods In the studied approach, electron density is calculated with a one‐parametric linear superposition (‘alpha blending’) of the two DECT images, which is shown to be equivalent to an affine relation between the photon attenuation cross sections of the two x‐ray energy spectra. We propose to use the latter relation for empirical calibration of the spectrum‐dependent blending parameter. For a conclusive assessment of the electron density uncertainty, we chose to isolate the purely methodological uncertainty component from CT‐related effects such as noise and beam hardening. Results Analyzing calculated spectrally weighted attenuation coefficients, we find universal applicability of the investigated approach to arbitrary mixtures of human tissue with an upper limit of the methodological uncertainty component of 0.2%, excluding high‐Z elements such as iodine. The proposed calibration procedure is bias‐free and straightforward to perform using standard equipment. Testing the calibration on five published data sets, we obtain very small differences in the calibration result in spite of different experimental setups and CT protocols used. Employing a general calibration per scanner type and voltage combination is thus conceivable. Conclusion Given the high suitability for clinical application of the alpha‐blending approach in combination with a very small methodological uncertainty, we conclude that further refinement of image‐based DECT‐algorithms for electron density assessment is not advisable.
Isolation of anaerobic respiratory mutants of Shewannella putrefaciens and genetic analysis of mutants deficient in anaerobic growth on Fe3+

A genetic approach was used to study (dissimilatory) ferric iron (Fe3+) reduction in Shewanella putrefaciens 200. Chemical mutagenesis procedures and two rapid plate assays were developed to facilitate the screening of Fe3+ reduction-deficient mutants. Sixty-two putative Fe3+ reduction-deficient mutants were identified, and each was subsequently tested for its ability to grow anaerobically on various compounds as sole terminal electron acceptors, including Fe3+, nitrate (NO3-), nitrite (NO2-), manganese oxide (Mn4+), sulfite (SO3(2-)), thiosulfate (S2O3(2-)), trimethylamine N-oxide, and fumarate. A broad spectrum of mutants deficient in anaerobic growth on one or more electron acceptors was identified. Nine of the 62 mutants (designated Fer mutants) were deficient only in anaerobic growth on Fe3+ and retained the ability to grow on all other electron acceptors. These results suggest that S. putrefaciens expresses at least one terminal Fe3+ reductase that is distinct from other terminal reductases coupled to anaerobic growth. The nine Fer mutants were conjugally mated with an S. putrefaciens genomic library harbored in Escherichia coli S17-1. Complemented S. putrefaciens transconjugants were identified by the acquired ability to grow anaerobically on Fe3+ as the sole terminal electron acceptor. All recombinant cosmids that conferred the Fer+ phenotype appeared to carry a common internal region.
Measurements of 3-dimensional Downslope Acoustic Propagation During the Basin Acoustic Seamount Scattering EXperiment (BASSEX-04)

As part of the North Pacific Acoustic Laboratory (NPAL) 2004 sea-test, the Basin Acoustic Seamount Scattering EXperimnet (BASSEX) was performed. A portion of this test was dedicated to taking towed array measurements of acoustic transmissions from the NPAL source moored off the coast of Kauai. In this paper, several transmissions which show evidence of 3-dimensional propagation are analyzed. Broadband transmissions to a towed array provide the opportunity to examine the spacial and temporal arrival structure of the acoustic propagation. Clear multipath arrivals with times and arrival angles different from the expected 2-dimensional plane of propagation are recorded. These results are presented as well as a hypothoses for how the interaction of the acoustic field and the local bathymetry leads to 3-dimensional propagation. In order to examine the stability of these arrivals, the 20 minute reception is run through a frequency domain adaptive beamformer. Comparison of the eigenspectra with 2 D Parabolic Equation simulations leads to the conclusion that bottom roughness and 3 D propagation are significant factors in explaining the arrival complexity.
Molecular cloning and expression in Escherichia coli of a cellodextrinase gene from Bacteroides succinogenes S85

A DNA fragment coding for a cellodextrinase of Bacteroides succinogenes S85 was isolated by screening of a pBR322 gene library in Escherichia coli HB101. Of 100,000 colonies screened on a complex medium with methylumbelliferyl-beta-D-cellobioside as the indicator substrate, two cellodextrinase-positive clones (CB1 and CB2) were isolated. The DNA inserts from the two recombinant plasmids were 7.7 kilobase pairs in size and had similar restriction maps. After subcloning from pCB2, a 2.5-kilobase-pair insert which coded for cellodextrinase activity was isolated. The enzyme was located in the cytoplasm of the E. coli host. It exhibited no activity on carboxymethyl cellulose, Avicel microcrystalline cellulose, acid-swollen cellulose, or cellobiose but hydrolyzed p-nitrophenyl-beta-D-cellobioside and p-nitrophenyl-beta-D-lactoside. The Km (0.1 mM) for the hydrolysis of p-nitrophenyl-cellobioside by the enzyme expressed in E. coli was similar to that reported for the purified enzyme from B. succinogenes. Expression of the cellodextrinase gene was subjected to catabolite repression by glucose and was not induced by cellobiose. The origin of the DNA insert from B. succinogenes was confirmed by Southern blot analysis. Western blotting (immunoblotting) using antibodies raised against the purified B. succinogenes cellodextrinase revealed a protein with a molecular weight of approximately 50,000 in E. coli clones which comigrated with the native enzyme isolated from B. succinogenes. These data indicate that the cellodextrinase gene expressed in E. coli is fully functional and codes for an enzyme with properties similar to those of the native enzyme.
High-Fiber Diet for Treatment of Constipation in Women With Pelvic Floor Disorders

OBJECTIVE: To examine the effect of high-fiber diet on constipation in women with pelvic floor disorders. METHODS: This was a study of a prospective cohort of 41 consecutive women presenting to a tertiary care facility for pelvic floor disorders with a complaint of constipation from March 2005 to September of 2005. Patient Assessment of Constipation Symptoms and Rome II criteria administered as a questionnaire were obtained through telephone interviews every 14 days and were evaluated at the end of the 42-day study period. Each patient was instructed to supplement her diet with a high-fiber cereal (14 g of fiber per one-half cup). Women gradually increased their cereal intake with a goal of reaching 28 g of fiber daily. Patients with adverse reactions, abdominal bloating or pain, and surgery during the study period were withdrawn. RESULTS: Median age and body mass index were 60 years (range 33–77 years), and 29.9 kg/m2 (range 21.6–59.8), respectively. Thirty patients (73%) completed the study. Average Rome II scores improved from day 1 to day 42 (P<.05). The total, abdominal, rectal, and stool symptoms of the Patient Assessment of Constipation Symptoms improved significantly during the study period (P<.001). Weekly laxative use and vaginal splinting were decreased from 2.8, 1.5 to 1.4, 0.67 (P<.05), respectively. CONCLUSION: Increasing fiber intake gradually to the amount recommended by the National Academy of Sciences Institute of Medicine improves constipation and its associated symptoms. Reducing the incidence and severity of straining in constipated women may help a risk factor for the onset, progression, or recurrence of prolapse. LEVEL OF EVIDENCE: III
A randomized, double-blind, parallel-group, placebo-controlled trial of Extract Sceletium tortuosum (Zembrin) in healthy adults.

OBJECTIVES The objective of the study was to evaluate the safety and tolerability of two doses (8 mg and 25 mg once daily) of a 2:1 standardized extract of the South African medicinal plant Sceletium tortuosum (L.) N.E. Br. , trademarked Zembrin,(®) in healthy adult volunteers over a three-month period. DESIGN This was a randomized, double-blind, parallel-group, placebo-controlled single center study. SETTING Tiervlei Trial Centre, Karl Bremer Hospital, Bellville, Cape Town, South Africa. PARTICIPANTS The study took place between February 2 and July 27, 2009. Thirty-seven healthy adults were recruited from the general population. INTERVENTION Participants were randomized to receive either one of two doses of study medication, or an identical placebo, taken once daily for 3 months. Of the 37 subjects, 12, 12, and 13 subjects received 8 mg extract Sceletium tortuosum (Zembrin), 25 mg extract Sceletium tortuosum (Zembrin), and placebo treatment, respectively. OUTCOME MEASURES No efficacy variables were assessed. The safety and tolerability variables comprised of vital signs, physical examination, 12-lead electrocardiogram (ECG), laboratory assessments (hematology, biochemistry, and urinalysis), and the recording of adverse events (AEs). RESULTS There were no apparent differences between the three treatments with regard to vital signs, 12-lead ECG, body weight, and physical examination from screening to the end of the 3-month treatment period. No significant changes were observed in hematology or biochemistry parameters between initial screening and the end of the study. Both doses of extract Sceletium tortuosum (Zembrin) were well-tolerated. The most commonly reported AE was headache, followed by abdominal pain and upper respiratory tract infections, all with greater incidence in the placebo group than in the treatment groups. Unsolicited positive effects on well-being were noted in patient diaries by some participants taking extract Sceletium tortuosum (Zembrin), including improved coping with stress and sleep. CONCLUSION Both doses of extract Sceletium tortuosum (Zembrin) (8 mg and 25 mg) were well tolerated when used by healthy human subjects once daily for 3 months.
Correlations between somatic features, anteroposterior spinal curvatures and trunk muscle strength in schoolchildren.

BACKGROUND Evaluation of body posture and strength of spinal muscles in children during their progressive ontogenesis is significant for the evaluation of their physical health condition and physical fitness. It is also a reference point in a process of control and medical care. PURPOSE The aim if this study was to evaluate correlation between the selected features of somatic body structure, shape of anteroposterior spinal curves and force-velocity (FV) parameters of trunk muscles in school children. PARTICIPANTS AND METHODS The sample involved 104 children aged 10-11 years, 60 females (10.74 ±0.7) and 44 males (10.50 ±0.9). Body posture was assessed using the Moiré photogrammetry while trunk muscles (flexors and extensors) strength was measured isokinetically. RESULTS The results of the research revealed the existence of many average and strong correlations observed between the analysed somatic characteristics and forcevelocity (FV) parameters of trunk muscles. Correlation between the volume of the spinal curvatures in the sagittal plane and forcevelocity parameters of trunk extensors and flexors were average or weak for both groups of children. CONCLUSION Somatic features indicated stronger correlation with trunk muscles' strength than with the size of the anteroposterior spinal curves.
Lung disease at diagnosis in infants with cystic fibrosis detected by newborn screening.

RATIONALE The promise of newborn screening (NBS) for cystic fibrosis (CF) has not been fully realized, and the extent of improvement in respiratory outcomes is unclear. We hypothesized that significant lung disease was present at diagnosis. OBJECTIVES To determine the extent of lung disease in a geographically defined population of infants with CF diagnosed after detection by NBS. METHODS Fifty-seven infants (median age, 3.6 mo) with CF underwent bronchoalveolar lavage and chest computed tomography (CT) using a three-slice inspiratory and expiratory protocol. MEASUREMENTS AND MAIN RESULTS Despite the absence of respiratory symptoms in 48 (84.2%) of infants, a substantial proportion had lung disease with bacterial infection detected in 12 (21.1%), including Staphylococcus aureus (n = 4) and Pseudomonas aeruginosa (n = 3); neutrophilic inflammation (41. 4 x 10(3) cells/ml representing 18.7% of total cell count); proinflammatory cytokines, with 44 (77.2%) having detectable IL-8; and 17 (29.8%) having detectable free neutrophil elastase activity. Inflammation was increased in those with infection and respiratory symptoms; however, the majority of those infected were asymptomatic. Radiologic evidence of structural lung disease was common, with 46 (80.7%) having an abnormal CT; 11 (18.6%) had bronchial dilatation, 27 (45.0%) had bronchial wall thickening, and 40 (66.7%) had gas trapping. On multivariate analysis, free neutrophil elastase activity was associated with structural lung disease. Most children with structural lung disease had no clinically apparent lung disease. CONCLUSIONS These data support the need for full evaluation in infancy and argue for new treatment strategies, especially those targeting neutrophilic inflammation, if the promise of NBS for CF is to be realized.
Autophagy and p62 in Cardiac Proteinopathy

Rationale: Recent studies suggest an important role of autophagy in protection against &agr;B-crystallin-based (CryABR120G) desmin-related cardiomyopathies (DRC), but this has not been demonstrated in a different model of cardiac proteinopathy. Mechanisms underlying the response of cardiomyocytes to proteotoxic stress remain incompletely understood. Objective: Our first objective was to determine whether and how the autophagic activity is changed in a mouse model of desminopathy. We also investigated the role of p62 in the protein quality control of cardiomyocytes. Methods and Results: Using an autophagosome reporter and determining changes in LC3-II protein levels in response to lysosomal inhibition, we found significantly increased autophagic flux in mouse hearts with transgenic overexpression of a DRC-linked mutant desmin. Similarly, autophagic flux was increased in cultured neonatal rat ventricular myocytes (NRVMs) expressing a mutant desmin. Suppression of autophagy by 3-methyladenine increased, whereas enhancement of autophagy by rapamycin reduced the ability of a comparable level of mutant desmin overexpression to accumulate ubiquitinated proteins in NRVMs. Furthermore, p62 mRNA and protein expression was significantly up-regulated in cardiomyocytes by transgenic overexpression of the mutant desmin or CryABR120G both in intact mice and in vitro. The p62 depletion impaired aggresome and autophagosome formation, exacerbated cell injury, and decreased cell viability in cultured NRVMs expressing the misfolded proteins. Conclusions: Autophagic flux is increased in desminopathic hearts, and as previously suggested in CryABR120G-based DRC, this increased autophagic flux serves as an adaptive response to overexpression of misfolded proteins. The p62 is up-regulated in mouse proteinopathic hearts. The p62 promotes aggresome formation and autophagy activation and protects cardiomyocytes against proteotoxic stress.
A comparison of the physiological response to simulated altitude exposure and r-HuEpo administration

Concerns have been raised about the morality of using simulated altitude facilities in an attempt to improve athletic performance. One assumption that has been influential in this debate is the belief that altitude houses simply mimic the physiological effects of illegal recombinant human erythropoietin (r-HuEpo) doping. To test the validity of this assumption, the haematological and physiological responses of 23 well-trained athletes exposed to a simulated altitude of 2650-3000 m for 11-23 nights were contrasted with those of healthy volunteers receiving a low dose (150 IU·kg-1 per week) of r-HuEpo for 25 days. Serial blood samples were analysed for serum erythropoietin and percent reticulocytes; maximal oxygen uptake ([Vdot]O2max) was assessed before and after r-HuEpo administration or simulated altitude exposure. The group mean increase in serum erythropoietin (422% for r-HuEpo vs 59% for simulated altitude), percent reticulocytes (89% vs 30%) and [Vdot]O2max (6.6% vs -2.0%) indicated that simulated altitude did not induce the changes obtained with r-HuEpo administration. Based on the disparity of these responses, we conclude that simulated altitude facilities should not be considered unethical based solely on the tenet that they provide an alternative means of obtaining the benefits sought by illegal r-HuEpo doping.
Influence of shade timing on an Equisetum arvense L. population

Equisetum arvense L. is a perennial pteridophyte that grows in open sites. In Tokyo, the plant has photosynthetic shoots from late March to November. However, in some populations, these shoots are lost before summer because of shading by taller plants. To investigate the contribution of shoots that remain on the plant for a certain duration, in terms of the maintenance of the E. arvense population, tubers were cultivated under different light conditions and the dry weight of growth, photosynthetic rates and respiration rates were measured. Individual growth was simulated on the basis of matter production and its partitioning. Biomass at the start of the next growing season (the initial size) was seriously decreased by shading before July. However, shading after July had little effect on the initial size of the next season plants. Thus, E. arvense can maintain its population if its shoots are retained until summer.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 824 Benefits of Spontaneous Breathing Compared with Mechanical Ventilation

Vimláti, L. 2012. Benefits of Spontaneous Breathing: Compared with Mechanical Ventilation. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 824. 47 pp. Uppsala. ISBN 978-91-554-8498-9. When spontaneous breathing (SB) is allowed during mechanical ventilation (MV), atelectatic lung areas are recruited and oxygenation improves thereby. Whether unsupported SB at its natural pattern (without PEEP and at low pressure/small tidal volume) equally recruits and improves oxygenation, and if so by which mechanism, has not been studied. A porcine lung collapse model was designed to study this question. The cardiac output dependency of the pulmonary shunt was investigated with healthy lungs and with major shunt (during one-lung ventilation) and with SB, MV and continuous positive airway pressure (CPAP). The hypoxic pulmonary vasoconstriction (HPV) was blocked with sodium nitroprusside (SNP) to see whether HPV is the only mechanism available for ventilation/perfusion (VA/Q) matching during MV and SB. In all experiments, respiratory rate and tidal volume during MV were matched to SB. Oxygenation was assessed by serial blood gas measurements, recruitment by thoracic CTs; pulmonary shunt was assessed by multiple inert gas elimination or venous admixture. SB attained better oxygenation and lower pulmonary shunt compared with MV, although it did not recruit collapsed lung. Pulmonary shunt did not correlate with cardiac output during SB, whereas a correlation was found during MV and CPAP. With blocked HPV, pulmonary shunt was considerably lower during SB than MV. In conclusion, SB improves VA/Q matching as compared with MV, even when no recruitment occurs. In contrast to MV and CPAP, cardiac output has no major effect on pulmonary shunt during SB. The improved VA/Q matching during SB despite a blocked HPV might indicate the presence of a SB-specific mechanism that improves pulmonary blood flow redistribution towards ventilated lung regions independent of or supplementary to HPV.
Relationship between Time-to-ROSC and Survival in Out-of-hospital Cardiac Arrest ECPR Candidates: When is the Best Time to Consider Transport to Hospital?

Abstract Objective: Extracorporeal cardiopulmonary resuscitation (ECPR) may improve outcomes for refractory out-of-hospital cardiac arrest (OHCA). Transport of intra-arrest patients to hospital however, may decrease CPR quality, potentially reducing survival for those who would have achieved return-of-spontaneous-circulation (ROSC) with further on-scene resuscitation. We examined time-to-ROSC and patient outcomes for the optimal time to consider transport. Methods: From a prospective registry of consecutive adult non-traumatic OHCA's, we identified a hypothetical ECPR-eligible cohort of EMS-treated patients with age ≤ 65, witnessed arrest, and bystander CPR or EMS arrival < 10 minutes. We assessed the relationship between time-to-ROSC and survival, and constructed a ROC curve to illustrate the ability of a pulseless state to predict non-survival with conventional resuscitation. Results: Of 6,571 EMS-treated cases, 1,206 were included with 27% surviving. Increasing time–to–ROSC (per minute) was negatively associated with survival (adjusted OR 0.91; 95%CI 0.89–0.93%). The yield of survivors per minute of resuscitation increased from commencement and started to decline in the 8th minute. Fifty percent and 90% of survivors had achieved ROSC by 8.0 and 24 min, respectively, at which times the probability of survival for those with initial shockable rhythms was 31% and 10%, and for non-shockable rhythms was 5.2% and 1.6%. The ROC curve illustrated that the 16th minute of resuscitation maximized sensitivity and specificity (AUC = 0.87, 95% CI 0.85–0.89). Conclusion: Transport for ECPR should be considered between 8 to 24 minutes of professional on-scene resuscitation, with 16 minutes balancing the risks and benefits of early and later transport. Earlier transport within this window may be preferred if high quality CPR can be maintained during transport and for those with initial non-shockable rhythms.