Miracle-dz/UniFAR-FTUs huggingface dataset:
Serological and molecular capsular typing, antibiotic susceptibility and multilocus sequence typing of Streptococcus pneumoniae isolates from invasive and non‐invasive infections

Background Streptococcus pneumoniae (S. pneumoniae) is a major causative agent of severe infections, including sepsis, pneumonia, meningitis, and otitis media, and has become a major public health concern. We report the pneumococcal serotype and sequence type (ST) distribution, and antimicrobial resistance of 39 S. pneumoniae strains from seven hospitals in China. Methods Blood/cerebrospinal fluid (CSF) and sputum isolates from patients were analyzed to determine S. pneumoniae serotypes by polymerase chain reaction (PCR) and the Neufeld Quellung reaction, the multilocus sequence types (MLST) by PCR and sequencing, and susceptibility to antimicrobial agents by the VITEK Gram Positive Susceptibility Card. Results A total of 39 isolates were collected including 21 blood/CSF and 18 sputum isolates. Conventional serotyping by the Quellung reaction required 749 reactions. In contrast, PCR based typing needed only 106 PCR reactions. The most frequent serotypes from the blood/CSF isolates were 14 (38.1%), 19A (14.3%), 23F (9.5%), and 18C (9.5%). In the sputum isolates the most frequent serotypes were 19F (33.3%), 23F (16.7%), 19A (11.1%), and 3 (11.1%). The incidence of penicillin resistance in the blood/CSF and sputum isolates was 66.7% and 55.6%, respectively. Statistical analysis showed that patients ≤5 years old had a higher resistance to penicillin when they compared with the patients ≥65 years old (P=0.011). Serotypes 14, 19A and 19F were significantly associated with penicillin resistance (P <0.001). ST320, ST271, and ST876 isolates showed high resistant rates to several antibiotics including penicillin (P=0.006). All of the isolates of serotype 19A were resistant to both penicillin and erythromycin, and they were all multi‐drug resistant (MDR) isolates. Conclusions The specificity and sensitivity of multiplex‐PCR are good, and this method represents a substantial savings of time and money, and can be widely used in the laboratory and clinical practice. Data from this research showed an extremely high prevalence of penicillin resistance and an increasing prevalence of multi‐drug resistant (MDR) rate in S. pneumoniae. A distinctive emergence of serotype 19A was observed which was also associated with the increasing prevalence of antimicrobial resistance. Therefore, nationwide surveillance of pneumococcal resistance and serotypes is strongly warranted.
Human neutrophil elastase induces MUC5AC overexpression in chronic rhinosinusitis through tumour necrosis factor-α converting enzyme

Abstract Conclusion The HNE–TACE signalling pathway has an important role in the process of MUC5AC overexpression in chronic rhinosinusitis (CRS). Objectives To provide evidence of HNE-induced MUC5AC overexpression in CRS via TACE. Method HE and PAS staining were used to assess the pathological changes in sinus mucosa samples from CRS or normal control. HNE, TACE, and MUC5AC expression in the sinonasal mucosa was determined using immunohistochemistry (IHC) and real-time polymerase chain reaction (qRT-PCR). In addition, the MUC5AC and TACE expression was determined in a primary culture of human nasal mucosa epithelial cells in vitro. Results On HE staining, the main pathological feature in the sinus mucosa of CRS patients was hyperplasia of goblet cells, inflammatory cells, and submucosal glands. Mucosa from the two experimental groups also showed strong expression on PAS staining. IHC and qRT-PCR demonstrated that HNE, TACE, and MUC5AC expression was significantly higher in the CRS patients compared with control samples (p < 0.05). MUC5AC mRNA expression was higher in cells stimulated by HNE than in untreated cells (p < 0.05). MUC5AC mRNA expression was significantly reduced in cells pre-treated with the TACE inhibitor TAPI-1 prior to HNE stimulation, compared with untreated and HNE-stimulated cells (p < 0.01).
Validity and sensitivity to change of the Patient Specific Functional Scale used during rehabilitation following proximal humeral fracture

Abstract Purpose: To describe content validity, concurrent validity, sensitivity to change, internal consistency and the outcome distribution of the Patient Specific Functional Scale (PSFS) in patients with proximal humeral fracture. Method: Fifty-three patients with proximal humeral fracture treated conservatively or surgically with plate and screw or intramedullary nail were recruited 6 weeks (±1 week) post-trauma or post-surgery. The following assessments were used: the PSFS, patient global score, shoulder function assessment, grip strength and Western Ontario Osteoarthritis of the shoulder Index (WOOS), before start of (n = 53) and after (n = 22) 2–3 months of group rehabilitation. Results: In total, 96% of the activities stated in the PSFS was classified in the International Classification of Functioning, Disability and Health activity component and 62% were found in the WOOS. Correlations between measures were low. The PSFS was highly sensitive to change to a period of group rehabilitation. All questions of the PSFS contributed to the total score. Both floor and ceiling effects could be noted. Conclusion: The PSFS shows satisfying measurement properties and may be a useful complement in the evaluation of individual changes during a period of rehabilitation after proximal humeral fracture. Implications for Rehabilitation The PSFS assesses on activity level in patients with proximal humeral fracture. The PSFS is sensitive to change for group rehabilitation after humeral fracture. The PSFS can be useful for goal-setting, motivating and individually tailoring rehabilitation activities. The PSFS should be used in addition to specific measures of body functions and general health.
Memory dysfunction in epilepsy patients as a derangement of normal physiology.

Patients with CPS often display recent memory deficits. Typically, general intelligence, perceptual skills, language, remote memory, and primary memory are all normal. However, the ability to learn new combinations of cognitively complex material is deficient. This deficit may be specific for verbal material (e.g., as a difficulty with learning to recall a response word given an unrelated cue word), for nonverbal material (e.g., as a difficulty in drawing a complex figure from memory), or for both verbal and nonverbal material. Because these characteristics are typical of memory deficits after MTL damage, it is reasonable to suspect that these deficits in patients with epilepsy also reflect MTL damage. In many cases, MTL damage is apparent from neuroimaging studies, whereas seizure semiology suggests MTL onset. In these patients, the same pathology might be the cause of both the ictus and memory deficits. In other cases, memory impairment appears to be secondary to seizures. This suggestion is supported by cases where prolonged complex partial status resulted in a permanent global amnesia. Cases with shorter-lasting memory deficits were also presented. Neuropsychological testing revealed specific recent-memory deficits that cleared 2 weeks after a flurry of CPS and 24 hr after a single seizure. Depth recordings have demonstrated that MTL electrographic seizures can occur without subjective manifestations. When these are evoked by local electrical stimulation, a profound inability to learn new material may be observed during the afterdischarge. Similarly, artificially induced MTL spike-and-wave complexes interfere with the memory for simultaneously presented complex visual scenes. Recent evidence suggests that all of the above phenomena may reflect the engagement by epileptiform processes of the association-cortex (AC)-MTL circuits used in normal human memory. In recent memory tasks, cognitive evoked-potential components N4 and P3 are generated in the MTL and to a lesser degree in related AC regions. The N4/P3 are strongly modulated by familiarity in recent memory. This modulation is eliminated by anterior temporal lobectomy. The typical slow wave following spontaneous MTL interictal spikes has the same MTL voltage topography, and thus probably similar synaptic generators, as the cognitive P3 potential. Furthermore, MTL spike-and-wave complexes can be evoked in recent memory tasks at a fixed latency equal to that of the N4. (ABSTRACT TRUNCATED AT 400 WORDS)
Interpersonal Psychotherapy for Women With Comorbid Depression and Chronic Pain

Chronic pain is prevalent among patients with depression and a risk factor for poor depression treatment outcomes. No known psychotherapy approaches have been developed to target the needs of patients with comorbid depression and chronic pain. This study's goals were to evaluate feasibility, acceptability, and initial effects of interpersonal psychotherapy adapted for women with depression and chronic pain. Seventeen women with major depression and chronic pelvic pain were offered 8 sessions of individual treatment, interpersonal psychotherapy for depression and pain (IPT-P). Participants were recruited from a women's health clinic, were predominantly low-income and minority, and generally did not initially self-identify as depressed. Large effect sizes with significant improvements were found for depression severity and social adjustment; pain interference remained unchanged. Most enrolled patients reported a high level of satisfaction with IPT-P. This pilot study provides preliminary support for the use of IPT-P for patients with comorbid depression and chronic pain.
En Face Swept-Source Optical Coherence Tomography Detecting Thinning of Inner Retinal Layers as an Indicator of Capillary Nonperfusion

Purpose To report en face swept-source optical coherence tomography (SS-OCT) as a noninvasive detection modality for regions of retinal layer thinning that are potential indicators of retinal nonperfusion areas (NPAs) in patients with branch retinal vein occlusion (BRVO). Methods Thirty-one eyes of 46 patients with BRVO showing a definite retinal NPA larger than 1 disc in diameter within the vascular arcades were included in this study. We calculated the overlapping correspondence ratio between presumed NPA, which appeared as a dark area in en face SS-OCT, and definite NPA in corresponding fluorescein angiography (FA) images. The correlation between brightness in en face SS-OCT images and corresponding ganglion cell complex (GCC) thickness determined by SD-OCT GCC maps was evaluated as well. Results Measured NPA size in FA and presumed NPA size in en face SS-OCT showed strong correlation (r = 0.746, p<0.001) and colocalization. Reliable agreement between the 2 methods was confirmed by size comparisons (p = 0.11), with an overlapping correspondence ratio of 0.73. Conclusions The results suggest that en face SS-OCT is a noninvasive and relatively reliable method for delineating retinal thinning as an indicator of NPAs in eyes with BRVO. Because SS-OCT can be performed without mydriasis, this procedure may be an option for evaluating NPAs on a screening basis and during follow-up to reduce the number of FA examinations that carry very rare, but potentially fatal, allergic side effects.
Simulating exciton delocalization in organic solar cells by a modified drift-diffusion model

In order to understand the device physics and optimize the power conversion efficiency of organic solar cells (OSCs), the theoretical modeling involving the advanced excitonic physics is highly important. In this work, a modified drift-diffusion model is established to describe the exciton delocalization mechanism in the charge-generation process of the OSCs. The carrier transport, recombination and collection are also incorporated to fully capture the electrical response. The increase of the exciton delocalization ratio is demonstrated to be important for reducing the energy loss in the exciton dissociation process; and consequently, improving the device efficiency especially for the short-circuit current.
Prognostic indicators in a Danish hospital-based population of colic horses.

A prospective survey of 528 colic horses, referred to the Large Animal Hospital at the Royal Veterinary and Agricultural University of Copenhagen, Denmark, during the period August 1994 to December 1998, was undertaken to develop a predictive model for application in the clinical assessment of prognosis. In the multivariate logistic regression analysis, 357 colic cases were used in the elaboration of a simple clinical-practical model consisting of degree of pain, packed cell volume, capillary refill time and rectal temperature. The relationship between rectal temperature and outcome (survival/death) has been regarded as linear. It has also been reported to be nonsignificant. The present study suggests a strong U-shaped relation, which is easily transformed into a linear association and readily interpretable in the clinical situation if treated as a deviation from 38 degrees C. Several other clinical and laboratory variables were strongly related to outcome in the bivariate analysis. The changes in sensitivity and specificity of the multivariate model, when applied as a prognostic test, were presented with changing cut-off values. The cut-off value is the level, of predicted probability of death, at which the clinical decision to treat or subject to euthanasia is taken. The predictive performance of the model was further illustrated using a mortality of 19%. The optimal accurate classification for both survival and death was 87%, which was attained when a cut-off value of 86% was selected. To minimise the number of horses unnecessarily subjected to euthanasia, the cut-off value was increased. However, this simultaneously increased the number of misclassified survivors, i.e. the number of horses that would die despite treatment. Outcome was especially poorly predicted in 4 horses, as was indicated by extreme deviance residuals. In 2 of these horses the large residuals were attributable to sudden and severe changes in the course of disease. All 4 horses had changes in variable values towards abnormality prior to death. Repeated measurements are therefore suggested in order to increase the test performance in general. The prerequisites of clinical application of prognostic models are critically discussed. The main findings of the present study indicate that degree of pain, packed cell volume, capillary refill time and temperature deviation from 38 degrees C, used in a logistic regression model, offer a strong model for clinical assessment of prognosis.
Somatostatin receptor subtypes sst1 and sst2 elicit opposite effects on the response to glutamate of mouse hypothalamic neurones: an electrophysiological and single cell RT‐PCR study

We have previously shown that somatostatin can either enhance or decrease AMPA/kainate receptor‐mediated responses to glutamate in mouse‐dissociated hypothalamic neurones grown in vitro. To investigate whether this effect is due to differential activation of somatostatin (SRIF) receptor subtypes, we compared modulation of the response to glutamate by SRIF with that induced by CH‐275 and octreotide, two selective agonists of sst1 and sst2/sst5 receptors, respectively. Somatostatin either significantly decreased (49%) or increased (30%) peak currents induced by glutamate, and was ineffective in the remaining cells. Only the decreased response was obtained with octreotide, whereas only increased responses were elicited by CH‐275 (47 and 35% of the tested cells, respectively). Mean amplitude variations under somatostatin or octreotide on the one hand, and under somatostatin or CH‐275 on the other hand, were equivalent. Pertussis toxin pretreatment significantly decreased the number of cells inhibited by somatostatin or octreotide, but had no effect on the frequency of neurones showing increased sensitivity to glutamate during somatostatin or CH‐275 application. About half of the neurones tested by single cell reverse transcriptase polymerase chain reaction (RT‐PCR) expressed only one sst receptor (sst1 in 26% and sst2 in 22% of studied cells). Out of the remaining neurones, 34% displayed neither sst1 nor sst2 mRNAs, whereas 18% showed a simultaneous expression of both mRNA subtypes. Expression of sst1 or sst2 mRNA subtypes matched totally with the effects of somatostatin on sensitivity to glutamate in 79% of the neurones processed for PCR after recordings. These data show that pertussis toxin‐insensitive activation of the sst1 receptor subtype mediates somatostatin‐induced increase in sensitivity to glutamate, whereas decrease in the response to glutamate is linked to pertussis toxin‐sensitive activation of the sst2 receptor subtype.
Four Inserts within the Catalytic Domain Confer Extra Stability and Activity to Hyperthermostable Pyrolysin from Pyrococcus furiosus

ABSTRACT Pyrolysin from the hyperthermophilic archaeon Pyrococcus furiosus is the prototype of the pyrolysin family of the subtilisin-like serine protease superfamily (subtilases). It contains four inserts (IS147, IS29, IS27, and IS8) of unknown function in the catalytic domain. We performed domain deletions and showed that three inserts are either essential (IS147 and IS27) or important (IS8) for efficient maturation of pyrolysin at high temperatures, whereas IS29 is dispensable. The large insert IS147 contains Ca3 and Ca4, two calcium-binding Dx[DN]xDG motifs that are conserved in many pyrolysin-like proteases. Mutagenesis revealed that the Ca3 site contributes to enzyme thermostability and the Ca4 site is necessary for pyrolysin to fold into a maturation-competent conformation. Mature insert-deletion variants were characterized and showed that IS29 and IS8 contribute to enzyme activity and stability, respectively. In the presence of NaCl, pyrolysin undergoes autocleavage at two sites: one within IS29 and the other in IS27. Disrupting the ion pairs in IS27 and IS8 induces autocleavage in the absence of salts. Interestingly, autocleavage products combine noncovalently to form an active, nicked enzyme that is resistant to SDS and urea denaturation. Additionally, a single mutation in IS29 increases resistance to salt-induced autocleavage and further increases enzyme thermostability. Our results suggest that these extra structural elements play a crucial role in adapting pyrolysin to hyperthermal environments. IMPORTANCE Pyrolysin-like proteases belong to the subtilase superfamily and are characterized by large inserts and long C-terminal extensions; however, the role of the inserts in enzyme function is unclear. Our results demonstrate that four inserts in the catalytic domain of hyperthermostable pyrolysin contribute to the folding, maturation, stability, and activity of the enzyme at high temperatures. The modification of extra structural elements in pyrolysin-like proteases is a promising strategy for modulating global structure stability and enzymatic activity of this class of protease.
Active Impedance of Infinite Parallel-Fed Continuous Transverse Stub Arrays

This paper introduces a rigorous and effective modeling framework for the continuous transverse stub (CTS) array, based on a spectral Green's function approach. A multimodal expansion of the equivalent currents over the slots is used to derive an accurate expression for the active impedance of an infinite array. This formula is validated through comparisons with full-wave simulations when the array scans are in principal planes. The mathematical formulation highlights the broadband properties of CTS arrays and accurately predicts the impact of the geometrical parameters on the active impedance, as a function of frequency and scan angle. The discussion of the results provides physical insights to outline effective design strategies.
Systematic investigation of ion suppression and enhancement effects of fourteen stable-isotope-labeled internal standards by their native analogues using atmospheric-pressure chemical ionization and electrospray ionization and the relevance for multi-analyte liquid chromatographic/mass spectrometric

In clinical and forensic toxicology, multi-analyte procedures are very useful to quantify drugs and poisons of different classes in one run. For liquid chromatographic/tandem mass spectrometric (LC/MS/MS) multi-analyte procedures, often only a limited number of stable-isotope-labeled internal standards (SIL-ISs) are available. If an SIL-IS is used for quantification of other analytes, it must be excluded that the co-eluting native analyte influences its ionization. Therefore, the effect of ion suppression and enhancement of fourteen SIL-ISs caused by their native analogues has been studied. It could be shown that the native analyte concentration influenced the extent of ion suppression and enhancement effects leading to more suppression with increasing analyte concentration especially when electrospray ionization (ESI) was used. Using atmospheric-pressure chemical ionization (APCI), methanolic solution showed mainly enhancement effects, whereas no ion suppression and enhancement effect, with one exception, occurred when plasma extracts were used under these conditions. Such differences were not observed using ESI. With ESI, eleven SIL-ISs showed relevant suppression effects, but only one analyte showed suppression effects when APCI was used. The presented study showed that ion suppression and enhancement tests using matrix-based samples of different sources are essential for the selection of ISs, particularly if used for several analytes to avoid incorrect quantification. In conclusion, only SIL-ISs should be selected for which no suppression and enhancement effects can be observed. If not enough ISs are free of ionization interferences, a different ionization technique should be considered.
Antiviral medication use in a cohort of pregnant women during the 2009–2010 influenza pandemic

Abstract Preventing influenza-like illness (ILI) during pregnancy with antiviral medication use (AVMU) can mitigate serious health risks to mother and foetus. We report on AVMU in pregnant women in Ontario, Canada, and describe characteristics of AVMU during the 2009–2010 H1N1 pandemic. Rates and risk estimates of AVMU were compared across multiple categories and stratified across ILI infection status. Increased AVMU was observed in women with influenza infections, active smokers, those vaccinated against influenza, and those with pre-existing co-morbidities. Decreased AVMU was observed in women with multiple gestations, and those in neighbourhoods of high immigrant concentrations. Our stratified analysis indicated that the observed patterns differed by ILI infection status. We demonstrated that once infected, women across multiple groups were equally likely to use antiviral medications. In this report we also propose possible clinical explanations for the observed differences in AVMU, which will be useful in planning prevention initiatives for future pandemics.
A utility-based approach for customised cloud service selection

The fact that cloud computing is widely accepted results in an increasing number of cloud providers. Customers are now burdened with the task of deciding which provider to choose for serving their requirements. This work developed a broker-based framework capable of automatically selecting cloud services based on user-defined requirement parameters and the service level agreement (SLA) attributes of the cloud providers. The goal is to help customers make clever decisions to achieve their best benefit. The framework contains components for decision making, cloud monitoring, user authentication, cloud access and SLA management. More specifically, we developed a utility-based, dynamic and flexible matching algorithm capable of maximising the users' profits. The matching algorithms as well as the entire framework were evaluated using a realistic simulation environment. Experimental results show that our utility-based approach performs well in terms of the matching quality and cost-saving.