Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic and Genotypic Relationships between Bartonella henselae Strains

The ubiquitous feline intraerythrocytic pathogen Bartonella henselae causes a range of important human infections, and seroprevalence in blood donors in Australia is around 5% (6). Two antigenically distinct subtypes have been described, named for the type strain (Houston-1) and the more recently recognized Marseille strain (5), which have characteristic DNA sequences in the 16S rRNA gene (rDNA) and the gltA (citrate synthase) gene (2, 3, 5). Culture of this fastidious, gram-negative bacterium is difficult, and serology is a primary diagnostic approach. A recent report that Houston-like strains (including Houston-1, 90-615, and SA-2) may be distinguished from serologically distinct Marseille-like strains (including URBHLLY-8, URBHLIE-9, Fizz, and CAL-1) by the faster migration of a characteristic band (ca. 29 kDa) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis and immunoblotting of whole-cell lysates is therefore particularly noteworthy (7). However, the SDS-PAGE data appear to contrast with previous publications from the same laboratory (8, 9) and others (11). We therefore compared local human isolates with the Houston-1 and Marseille strains and also found two closely related genotypes with corresponding patterns on SDS-PAGE of whole-cell lysates (Fig. ​(Fig.1). 1). All human strains appear to have either the 30-kDa band (Houston) or the 29-kDa band (Marseille), in agreement with earlier studies (10, 11). The agar-pitting colony phenotype and number of in vitro passages have no apparent influence (Fig. ​(Fig.11 and Table ​Table1). 1). However, a local feline strain of the type II (Marseille-like) 16S rDNA genotype has the faster-migrating (29-kDa) band and a gltA gene sequence typical of Houston strains, consistent with the considerable diversity known to exist in feline strains (1, 10) and illustrating a dissociation of the accepted genotype-phenotype relationships. The strains in the recent study (7) were all human isolates and were assigned to genotypes by individual sequencing of several genes, including groEL (12) and the 16S rDNA (3). While the 29- to 30-kDa antigen(s) may yet prove useful for serotyping of human isolates, it thus seems unlikely that reported inconsistencies in the data can be easily explained by phase variation or genotype. In addition, we have no reason to assume that the more diverse feline strains are all nonpathogenic in humans. For both of thesereasons, we therefore urge caution in adopting this promising target as a basis for serotype distinction until the picture is clearer. FIG. 1. Marseille and Houston types. Coomassie-stained SDS-PAGE of whole-cell lysates harvested from chocolate agar plates (grown at 35°C in 5% CO2). High-molecular-weight (lane 1 and left border) and low-molecular-weight (right border) markers are shown, . TABLE 1. B. henselae isolates used in this study
Changes on Tendon Stiffness and Clinical Outcomes in Athletes Are Associated With Patellar Tendinopathy After Eccentric Exercise.

OBJECTIVE Eccentric exercise is commonly used as a form of loading exercise for individuals with patellar tendinopathy. This study investigated the change of mechanical properties and clinical outcomes and their interrelationships after a 12-week single-legged decline-board exercise with and without extracorporeal shockwave therapy (ESWT). DESIGN Randomized controlled trial. SETTING Outpatient clinic of a university. PARTICIPANTS Thirty-four male in-season athletes with patellar tendinopathy for more than 3 months were randomized into exercise and combined groups. INTERVENTIONS The exercise group received a 12-week single-legged decline-squat exercise, and the combined group performed an identical exercise program in addition to a weekly session of ESWT in the initial 6 weeks. MAIN OUTCOME MEASURES Tendon stiffness and strain were examined using ultrasonography and dynamometry. Visual analog scale and Victoria Institute of Sports Assessment-patella (VISA-p) score were used to assess pain and dysfunction. These parameters were measured at preintervention and postintervention. RESULTS Significant time effect but no significant group effect on the outcome measures; significant reduction in tendon stiffness (P = 0.02) and increase in tendon strain (P = 0.00); and reduction of intensity of pain (P = 0.00) and dysfunction (P = 0.00) were observed. Significant correlations between changes in tendon stiffness and VISA-p score (ρ = -0.58, P = 0.05); alteration in tendon strain, pain intensity (ρ = -0.63, P = 0.03); and VISA-p score (ρ = 0.60, P = 0.04) were detected after the exercise program. CONCLUSIONS Eccentric exercise-induced modulation on tendon mechanical properties and clinical symptoms are associated in athletes with patellar tendinopathy.
Verification of European Subseasonal Wind Speed Forecasts

AbstractAnalysis of the forecasts and hindcasts from the ECMWF 32-day forecast model reveals that there is statistically significant skill in predicting weekly mean wind speeds over areas of Europe at lead times of at least 14–20 days. Previous research on wind speed predictability has focused on the short- to medium-range time scales, typically finding that forecasts lose all skill by the later part of the medium-range forecast. To the authors’ knowledge, this research is the first to look beyond the medium-range time scale by taking weekly mean wind speeds, instead of averages at hourly or daily resolution, for the ECMWF monthly forecasting system. It is shown that the operational forecasts have high levels of correlation (~0.6) between the forecasts and observations over the winters of 2008–12 for some areas of Europe. Hindcasts covering 20 winters show a more modest level of correlation but are still skillful. Additional analysis examines the probabilistic skill for the United Kingdom with the applica.
Plasma charge-induced corrosion of tungsten-plug vias in CMOS devices

Plasma charge-induced corrosion of tungsten plug vias, where part of the via surface is exposed to the chemical solution after metal-2 etch by photolithographic misalignment with upper metal lines, was investigated. Some electrochemical tests and plasma damage monitoring were done to study the corrosion mechanism. The configuration of circuits was also investigated to understand the pattern dependency of the plasma damage and the corrosion. It is believed that the positive charges on the metal lines and P/sup +/ active region of the PMOS, developed during dry etching and ashing, are enhancing the corrosion of tungsten during stripping. The plasma-less O/sub 3/ asher applied to the ashing process reduced the plasma damage and did not produce empty vias on the wafer.
Hemodynamic Response to Induction and Intubation: Propofol/Fentanyl Interaction

Background:When given as an intravenous bolus for induction of anesthesia, propofol can decrease postintubation hypertension but can also create moderate to severe postinduction, preintubatlon hypotension. The addition of fentanyl usually decreases the postintubation hypertension but can increase the propofol-lnduced preintubation hypotension. The goal of the study was to determine the relation between propofol and fentanyl doses and the hemodynamic changes postinduction, preintubation and postintubation. Methods:Twelve groups of 10 patients, ASA physical status 1 or 2, first received fentanyl 0, 2, or 4 µg · kg-1 and then 5 min later received propofol 2.0, 2.5, 3.0, or 3.5 mg · kg-1 as an intravenous bolus for induction of anesthesia. Arterial blood pressure was continuously monitored. The trachea was intubated 4 min after propofol administration. Results:The mean decrease In systolic blood pressure after propofol was 28 mmHg when no fentanyl was given, 53 mmHg after 2 µg · kg-1 of fentanyl (P<0.05 vs. no fentanyl), and 50 mmHg after 4 µg · kg-1 (P<0.05 vs. no fentanyl; no statistically significant difference 4 vs. 2 µg · kg-1). There was no statistically significant difference in hemodynamic response to intubation relative to propofol dose. Hemodynamic response to intubation was decreased by the administration of fentanyl; the mean increase of systolic blood pressure after intubation was 65 mmHg from preintubation value without fentanyl, 50 mmHg after 2 µg · kg-1, and 37 mmHg after 4 µg · kg-1 (P<0.05 for 2 and 4 µg · kg-1 vs. no fentanyl and for 4 vs. 2 µg · 'kg-1). Hemodynamic changes postintubation were not statistically different with increasing doses of propofol. Conclusions:Hemodynamic changes after induction with propofol or propofol/fentanyl, pre- or postintubation, are not modified when the propofol dose is Increased from 2 to 3.5 mg · kg-1. Maximal hypotension preintubation occurs with a fentanyl dose of 2 µg · kg-1, whereas the magnitude of postintubation hypertension is significantly decreased with an increase in the fentanyl dose to 4 µg · kg-1.
Spatial properties of retinal mosaics: An empirical evaluation of some existing measures

Abstract Mosaics of neurons are usually quantified by methods based on nearest-neighbor distance (NND). The commonest indicator of regularity has been the ratio of the mean NND to the standard deviation, here termed the ‘conformity ratio. ’ However, an accurate baseline value of this ratio for bounded random samples has never been determined; nor was its sampling distribution known, making it impossible to test its significance. Instead, significance was assessed from goodness-of-fit to a Rayleigh distribution, or from another ratio, that of the observed mean NND to an expected mean predicted by theory, termed the dispersion index. Neither approach allows for boundary effects that are common in experimental mosaics. Equally common are ‘missing’ neurons, whose effects on the statistics have not been studied. To address these deficiencies, random patterns and real neuronal mosaics were analyzed statistically. Ns independent random-point samples of size Np were generated for 13 Np values between 25 and 6400, where Ns × Np ≥ 144,000. Samples were generated with rectangular boundaries of aspect ratio 1:1, 1:5, and 1:10 to examine the influence of sample geometry. NND distributions, conformity ratios, and dispersion indices were computed for the resulting 45,997 independent random patterns. From these, empirical sampling distributions and critical values were determined. NND distributions for small-to-medium, bounded, random populations were shown to differ significantly from Rayleigh distributions. Thus, goodness-of-fit tests are invalid for most experimental mosaics. Charts are presented from which the significance of conformity ratios or dispersion indices can be read directly. The conformity ratio reacts conservatively to extremes of sample geometry, and provides a useful and safe test. The dispersion index is nonconservative, making its use problematic. Tests based on the theoretical distribution of the dispersion index are unreliable for all but the largest samples. Random deletions were also made from 33 real retinal ganglion cell mosaics. The mean NND, conformity ratio, and dispersion index were determined for each original mosaic and 36 independent samples at each of nine sampling levels, retaining between 90% and 10% of the original population. An exclusion radius, based on a spatial autocorrelogram, was also calculated for each of these 10,725 mosaic samples. The mean NND was moderately insensitive to undersampling, rising smoothly. The exclusion radius was remarkably insensitive. The conformity ratio and dispersion index fell steeply, sometimes failing to reach significance while half of the cells still remained. For the same 33 original mosaics, linear regression showed the exclusion radius to be 62 ± 3% of the mean NND.
Evaluation of the performance of a new compression system in patients with lymphoedema

In the acute phase of lymphoedema, patients require comprehensive decongestive therapy (CDT), which includes skin care, an exercise regimen, manual lymphatic drainage (MLD) and regular bandaging. This study was established to determine the effectiveness of a new system of bandage therapy, the 3M™ Coban™ 2 compression system. In total, 24 patients were entered into the study (12 from UK and 12 from Canada) with a variety of clinical presentations. The mean age of the groups was 57·4 years, which varied from 26 to 79 years. Body mass index (BMI) averaged 38·9 kg/m2, with a range from 22·7 to 67·5 kg/m2. Of the total, eight were women with arm lymphoedema, the remainder being men and women with lymphoedema of the lower limb. All were considered to be in need of CDT. After 19 days, the reduction of limb volume was measured, which indicated a mean limb volume reduction of 1210 ml (95% confidence interval, CI, 780–1641, P < 0·001). Leg affected patients experienced greater reduction than arm affected patients (1596 ml versus 438 ml), although both groups experienced significant reduction in limb volumes (both P < 0·001). Mean percentage changes in limb volume were 14·9% and 16·1% for legs and arms, respectively. The Measure Your Medical Outcome Profile questionnaire indicated significant improvement in symptoms considered important by the patient (P < 0·0001), which also led to improvements in skin quality by reducing skin thickness and firmness. The Coban 2 compression system provides good oedema reduction in both arms and legs to reduce limb volume and improvements in symptoms associated with lymphoedema.
Kinetics of the Neutralizing Antibody Response to Respiratory Syncytial Virus Infections in a Birth Cohort

The kinetics of respiratory syncytial virus (RSV) neutralizing antibodies following birth, primary and secondary infections are poorly defined. The aims of the study were to measure and compare neutralizing antibody responses at different time points in a birth cohort followed‐up over three RSV epidemics. Rural Kenyan children, recruited at birth between 2002 and 2003, were monitored for RSV infection over three epidemic seasons. Cord and 3‐monthly sera, and acute and convalescent sera following RSV infection, were assayed in 28 children by plaque reduction neutralization test (PRNT). Relative to the neutralizing antibody titers of pre‐exposure control sera (1.8 log10 PRNT), antibody titers following primary infection were (i) no different in sera collected between 0 and 0.4 months post‐infection (1.9 log10 PRNT, P = 0.146), (ii) higher in sera collected between 0.5 and 0.9 (2.8 log10 PRNT, P < 0.0001), 1.0–1.9 (2.5 log10 PRNT, P < 0.0001), and 2.0–2.9 (2.3 log10 PRNT, P < 0.001) months post‐infection, and (iii) no different in sera collected at between 3.0 and 3.9 months post‐infection (2.0 log10 PRNT, P = 0.052). The early serum neutralizing response to secondary infection (3.02 log10 PRNT) was significantly greater than the early primary response (1.9 log10 PRNT, P < 0.0001). Variation in population‐level virus transmission corresponded with changes in the mean cohort‐level neutralizing titers. It is concluded that following primary RSV infection the neutralizing antibody response declines to pre‐infection levels rapidly (∼3 months) which may facilitate repeat infection. The kinetics of the aggregate levels of acquired antibody reflect seasonal RSV occurrence, age, and infection history. J Med. Virol. 85:2020–2025, 2013. © 2013 The Authors. Journal of Medical Virology published by Wiley Periodicals, Inc.
Investigating critical thinking and knowledge construction in an interactive learning environment

Critical thinking and knowledge construction have become essential competencies for people in the new information age. In this study, we designed an interactive learning environment involving three forms of interaction: individual reflections, group collaboration and, class discussions. The purpose of this study was to investigate the extent to which the three forms of interaction promoted students' critical thinking and knowledge construction. Seventeen students at National Institute of Education of Singapore participated in this study. Their reflections and discussions were analyzed by following a content analysis approach. Results showed that writing reflections had potential to promote critical thinking but, not all students thought critically. Knowledge construction in groups and in class discussions happened at lower levels. This paper presents the conceptual framework, design specifications and evaluation results of the ILE. Implications of the results are discussed.
Intracervical sodium nitroprusside versus vaginal misoprostol in first trimester surgical termination of pregnancy: a randomized double-blinded controlled trial.

BACKGROUND Results from small-scale randomized studies on the effectiveness of different preparations of nitric oxide donors in cervical priming before first trimester termination of pregnancies are not consistent. We compared sodium nitroprusside gel to misoprostol, the standard agent for cervical priming in this randomized double-blinded controlled trial. METHODS Two hundred pregnant patients between 8 to 12 weeks admitted for surgical termination of pregnancy were recruited. They were randomized into either 400 microg vaginal misoprostol and intracervical placebo gel, or 10 mg intracervical sodium nitroprusside gel and placebo tablets 3 h before the procedure. The baseline cervical dilatation and cumulative force required to dilate the cervix from 4 to 9 mm were measured with a tonometer. Blood pressure was measured and side effects were assessed. RESULTS The cumulative force to dilate the cervix from 4 to 9 mm was significantly higher in the sodium nitroprusside group, and the difference remained when a sub-group analysis was performed according to parity. Baseline cervical dilatation, duration of operation and operative blood loss were all in favour of misoprostol. Transient drop in blood pressure was observed after sodium nitroprusside treatment. CONCLUSIONS Intracervical sodium nitroprusside is not as effective as misoprostol in cervical priming.
Actions for Verification of RC Structures with FRP Bars

The use of concrete reinforced with nonmetallic bars in composite materials, characterized by higher values of strength and by lower values of Young's modulus compared to steel, implies that the design of structures will be influenced almost exclusively by the serviceability limit state (SLS). This circumstance deserves some reflection on the values of the actions to be considered at the SLS and at the ultimate limit state (ULS). As the actual codes consider the same distribution of actions obtained by statistical methods, for the SLS and, amplified, for the ULS, it is necessary to reexamine from a probabilistic point of view the effective distributions of actions to be adopted for the two different limit states. This, which is obviously true for any kind of structure built with any material, becomes paramount for concrete structures with nonmetallic reinforcement. In this paper some possible statistical distributions of actions for the verification at the ULS and the statistical distribution of the sampl.
Distribution pattern of small RNA and degradome reads provides information on miRNA gene structure and regulation

Plant microRNAs (miRNAs) have an impact in the regulation of several biological processes such as development, growth and metabolism by negatively controlling gene expression at the post-transcriptional level. However, the role of these small molecules in the symbiotic interaction of plant roots and arbuscular mycorrhizal (AM) fungi remained elusive. To elucidate the role of miRNAs during AM symbiosis we used a deep sequencing approach to analyze the small RNA and degradome sequence tags of Medicago truncatula non-mycorrhizal and mycorrhizal roots. We identified 243 novel Medicago microRNAs and 118 mRNA cleavage targets of miRNA mature and star sequences. Several AM symbiosis-relevant genes were identified as miRNA targets. The transcript of MtNsp2, encoding a GRAS transcription factor involved in the nodule and mycorrhizal signaling pathway, is cleaved by a novel member of the miR171 gene family, namely miR171h. Here, we carried out a detailed analysis of the genomic structure of the MIR171h gene comprising our deep sequencing data. The results suggest a feedback circuit between mature miR171h and its own primary transcript showing the ability of this miRNA regulating itself.
Policy Bias and Agriculture: Partial and General Equilibrium Measures

The paper examines the impact of industrial protection, agricultural export taxes, and overvaluation of the exchange rate on the balance between the agricultural and nonagricultural sectors. Various agricultural terms-of-trade indices are constructed to measure the policy bias against agriculture in a computable general equilibrium (CGE) framework and compare the results with earlier partial equilibrium measures. Our results indicate that the partial equilibrium measures miss much of the action operating through indirect product and factor market linkages, while overstating the strength of the linkages between changes in the exchange rate and prices of traded goods on the agricultural terms of trade.
Mental Practice: Applying Motor PRACTICE and Neuroplasticity Principles to Increase Upper Extremity Function

The vast majority of stroke survivors exhibit residual impairments,1,2 with most reporting-associated quality of life decrements.3,4 The prevalence of these poststroke motor deficits and the overall burden of stroke are likely to rise exponentially attributable to an aging population and increases in the prevalence of many risk factors (eg, obesity, diabetes mellitus, smoking). 5,6 In light of these trends, several promising motor interventions have been introduced, with many targeting upper extremity (UE) hemiparesis, given its widely appreciated impact. Yet, although several of these approaches appear efficacious, few therapeutic approaches showing promise in animal or early human trials are fully translated to regular clinical practice.7 Consistently, many contemporary motor rehabilitation strategies require high duration contact time8 and costly equipment,9 preventing their widespread clinical application, except among specialized rehabilitation and academic medical centers. Mental practice involves repetitive cognitive rehearsal of physical movements in the absence of physical, voluntary attempts. From a practical perspective, mental practice constitutes an attractive alternative to other rehabilitative approaches because it does not require physical rehearsal, can be performed without direct supervision, and requires minimal expense and equipment, facilitating ease of use. The brain’s ability to respond to repetitive, learning-based strategies even years after injury and well into adulthood also makes mental practice a favorable match for stroke, which tends to be a disease of the aged and because survivors frequently exhibit residual impairments for years postictus. We speculated that repetitive mental practice use, shown to trigger the same neural areas and musculature as physical practice of the same tasks,10–14 would cause substantive neural and motor changes in stroke survivors with UE deficits. Although used for decades in sport and exercise settings, this laboratory was the first to apply mental practice to increase learning …
Toward Robust Revenue Management: Competitive Analysis of Online Booking

In this paper, we consider the revenue management problem from the perspective of online algorithms. This approach eliminates the need for both demand forecasts and a risk-neutrality assumption. The competitive ratio of a policy relative to a given input sequence is the ratio of the policy's performance to the offline optimal. Under the online algorithm approach, revenue management policies are evaluated based on the highest competitive ratio they can guarantee. We are able to define lower bounds on the best-possible performance and describe policies that achieve these lower bounds. We address the two-fare problem in greatest detail, but also treat the general multifare problem and the bid-price control problem.