Miracle-dz/UniFAR-FTUs huggingface dataset:
A review of 11 years of Stenotrophomonas maltophilia blood isolates at a tertiary care institute in Canada.

BACKGROUND Stenotrophomonas maltophilia has emerged as a significant nosocomial pathogen with increasing resistance to trimethoprim/sulphamethoxazole (TMP/SMX), the current drug of choice for treatment. OBJECTIVES To describe the microbiological and clinical characteristics of S maltophilia bloodstream infections (BSIs) over an 11-year period at a tertiary care centre in Canada. METHODS All adult S maltophilia BSIs from 1999 to 2009 in a 750-bed tertiary care teaching hospital (University of Alberta Hospital, Edmonton, Alberta) were identified through the infection control nosocomial infection surveillance program. Demographic and clinical data were extracted from the infection control database and from patient charts. Microbiological data were confirmed through the laboratory information system. RESULTS Twenty-five episodes of S maltophilia BSI (0.9% of all BSIs) involving 24 patients were identified between 1999 and 2009. The patient age range was 18 to 83 years (average 45.7 years). The majority were men (14 of 24 [58.3%]). The mean length of hospital stay was 83.3 days (range eight to 310 days). The rate of S maltophilia BSIs per 1000 admissions ranged from 0.04 to 0.22 (average 0.09). Greater than one-half of the episodes (13 of 25 [52%]) were admitted to the intensive care unit before BSI onset. Laboratory data were available for 24 of the 25 isolates. Polymicrobial infections were present in 11 of 24 (45.8%) patients. Resistance to TMP/SMX occurred in 8.3% of all infections. Fifteen per cent of isolates were resistant to ticarcillin/clavulanate. Mortality attributed to bacteremia was 16.7%. CONCLUSIONS In the University of Alberta Hospital, the rate of S maltophilia BSI remains low and constant, and TMP/SMX remains the drug of choice for treatment.
Cause‐Specific Cumulative Incidence Estimation and the Fine and Gray Model Under Both Left Truncation and Right Censoring

Summary The standard estimator for the cause‐specific cumulative incidence function in a competing risks setting with left truncated and/or right censored data can be written in two alternative forms. One is a weighted empirical cumulative distribution function and the other a product‐limit estimator. This equivalence suggests an alternative view of the analysis of time‐to‐event data with left truncation and right censoring: individuals who are still at risk or experienced an earlier competing event receive weights from the censoring and truncation mechanisms. As a consequence, inference on the cumulative scale can be performed using weighted versions of standard procedures. This holds for estimation of the cause‐specific cumulative incidence function as well as for estimation of the regression parameters in the Fine and Gray proportional subdistribution hazards model. We show that, with the appropriate filtration, a martingale property holds that allows deriving asymptotic results for the proportional subdistribution hazards model in the same way as for the standard Cox proportional hazards model. Estimation of the cause‐specific cumulative incidence function and regression on the subdistribution hazard can be performed using standard software for survival analysis if the software allows for inclusion of time‐dependent weights. We show the implementation in the R statistical package. The proportional subdistribution hazards model is used to investigate the effect of calendar period as a deterministic external time varying covariate, which can be seen as a special case of left truncation, on AIDS related and non‐AIDS related cumulative mortality.
Intrapartum Electronic Fetal Heart Rate Monitoring and the Prevention of Perinatal Brain Injury

OBJECTIVE: Electronic fetal heart rate monitoring (EFM) is the most widely used method of intrapartum surveillance, and our objective is to review its ability to prevent perinatal brain injury and death. DATA SOURCES: Studies that quantified intrapartum EFM and its relation to specific neurologic outcomes (seizures, periventricular leukomalacia, cerebral palsy, death) were eligible for inclusion. MEDLINE was searched from 1966 to 2006 for studies that examined the relationship between intrapartum EFM and perinatal brain injury using these MeSH and text words: “cardiotocography,” “electronic fetal monitoring,” “intrapartum fetal heart rate monitoring,” “intrapartum fetal monitoring,” and “fetal heart rate monitoring. ” METHODS OF STUDY SELECTION: This search strategy identified 1,628 articles, and 41 were selected for further review. Articles were excluded for the following reasons: in case reports, letters, commentaries, and review articles, intrapartum EFM was not quantified, or specific perinatal neurologic morbidity was not measured. Three observational studies and a 2001 meta-analysis of 13 randomized controlled trials were selected for determination of the effect of intrapartum EFM on perinatal brain injury. TABULATION, INTEGRATION, AND RESULTS: Electronic fetal monitoring was introduced into widespread clinical practice in the late 1960s based on retrospective studies comparing its use to historical controls where auscultation was performed in a nonstandardized manner. Case-control studies have shown correlation of EFM abnormalities with umbilical artery base excess, but EFM was not able to identify cerebral white matter injury or cerebral palsy. Of 13 randomized controlled trials, one showed a significant decrease in perinatal mortality with EFM compared with auscultation. Meta-analysis of the randomized controlled trials comparing EFM with auscultation have found an increased incidence of cesarean delivery and decreased neonatal seizures but no effect on the incidence of cerebral palsy or perinatal death. CONCLUSION: Although intrapartum EFM abnormalities correlate with umbilical cord base excess and its use is associated with decreased neonatal seizures, it has no effect on perinatal mortality or pediatric neurologic morbidity.
Vitamin and Mineral Supplement Use by Community-Dwelling Adults Living in Canada and the United States: A Scoping Review

ABSTRACT Vitamin and mineral supplements can assist a person in meeting recommended intakes but excessive use can pose risks. Knowing prevalence of supplement use is the first step toward gauging risk-benefit. This scoping review sought to determine the prevalence of vitamin and mineral supplement use among community-dwelling Canadian and American adults. Medline and Embase were searched using keywords and MeSH headings that encapsulated both vitamin and mineral supplements and community-dwelling adults in Canada and the United States. Search limits were set for study participants over the age of 18, English language articles, and a publication date from the year 2000 to June of 2016. Of the 181 articles originally identified, 30 were deemed relevant for this scoping review. Eleven studies reported on vitamin and mineral supplement use in general, without specifying the prevalence of use for any particular supplement(s). Prevalence of general vitamin and mineral supplement use reported in these studies ranged from 7-85%. Twenty-two studies reported the prevalence of consumption for specific vitamins and minerals; although three of these studies also reported on overall supplement use. Calcium and vitamin D were widely reported, with 10 of 22 studies focusing on these key nutrients. Multivitamin/mineral supplements were also widely studied with 8 of 22 articles reporting their prevalence of consumption. Results from this scoping review indicate that data on the quantity and combination of supplement use is lacking in Canada and United States. These data are key for identifying intake amounts and combinations that have the potential to cause adverse effects.
Antiviral therapy for “difficult‐to‐treat” hepatitis C virus‐infected patients

Objective To review the updated research on direct antiviral agents (DAAs)‐including regimens for hepatitis C virus (HCV), and focus on “difficult‐to‐treat” HCV‐infected patients. Data sources The literature concerning DAAs and hepatitis C cited in this review was collected from PubMed and Google Scholar databases published in English up to July 2013. Study selection Data from published articles regarding HCV and DAAs in clinical trials and in clinical use were identified and reviewed. Results It was recognized that some “difficult‐to‐treat” patients would still exist, even though stronger treatments using such as DAAs, including telaprevir and boceprevir, which lead to higher sustained virological response rates, are available. Such patients include those with advanced fibrosis/cirrhosis, elderly persons, children, HCV‐human immunodeficiency virus co‐infected patients, HCV‐infected recipients, and so on. Conclusions Certain “difficult‐to‐treat” patients would still exist, even though stronger treatment is available. Although evidence from clinical trials is still lacking, interferon‐sparing regimens could have stronger effects for eradicating HCV in such cases.
BSR guidelines on standards of care for persons with rheumatoid arthritis.

The aim is to develop nationally accepted measures for the delivery of care for persons with rheumatoid arthritis. These should usually be recorded as part of the normal clinical care of the patient. Specific situations in which patients may require closer than average monitoring are also discussed. The aim is to obtain the best quality of care within the resources available. The need for multidisciplinary team care is also addressed. The standards address the following areas:
Predictors of trying to lose weight among overweight and obese Mexican-Americans: a signal detection analysis

Abstract Objective Signal detection analysis, a form of recursive partitioning, was used to identify combinations of sociodemographic and acculturation factors that predict trying to lose weight in a community-based sample of 957 overweight and obese Mexican-American adults (ages 18–69 years). Design Data were pooled from the 2004 and 2006 Behavioral Risk Factor Surveillance System conducted in a low-income, semi-rural community in California. Results Overall, 59 % of the population reported trying to lose weight. The proportion of adults who were trying to lose weight was highly variable across the seven mutually exclusive groups identified by signal detection (range 30–79 %). Significant predictors of trying to lose weight included BMI, gender, age and income. Women who were very overweight (BMI > 28·5 kg/m2) were most likely to be trying to lose weight (79 %), followed by very overweight higher-income men and moderately overweight (BMI = 25·0–28·5 kg/m2) higher-income women (72 % and 70 %, respectively). Moderately overweight men, aged 28–69 years, were the least likely to be trying to lose weight (30 %), followed by moderately overweight lower-income women (47 %) and very overweight lower-income men (49 %). The latter group is of particular concern since they have characteristics associated with medical complications of obesity (low education and poor access to medical care). Conclusions Our findings highlight opportunities and challenges for public health professionals working with overweight Mexican-American adults – particularly lower-income adults who were born in Mexico – who are not trying to lose weight and are therefore at high risk for obesity-related co-morbidities.
A qualitative evaluation of questions and responses from five occupational questionnaires developed to assess exposures.

Questionnaires are increasingly being used in the workplace to assess exposures to chemicals and other agents. Although the literature contains much information on questionnaire design in general, little information is available on the challenges related to questionnaires applied to the occupational setting. Questionnaires on dry cleaning workers, nurses, farmers, car mechanics, and truck drivers were administered to a total of 25 people currently performing one of these jobs. After asking each question, the interviewer probed to identify the difficulties the respondents had in answering the questions. Overall, the respondents were able to answer the questions. Problems were found, however, with particular questions that reduced the effectiveness of the questionnaire. These included the use of unclear terms, questions open to multiple interpretations, difficult computational requirements (e.g., asking for averages for highly variable tasks), ineffective transitions between topics, and overlapping response categories. This type of testing is a crucial part of questionnaire development and can be used to effectively identify potential problems with questions and, therefore, improve them to enhance collection of higher-quality data for assessments of occupational exposures.
The Forkhead Transcription Factor FoxO Regulates Transcription of p27Kip1 and Bim in Response to IL-21

The cytokine IL-2 plays a very important role in the proliferation and survival of activated T cells. These effects of IL-2 are dependent on signaling through the phosphatidylinositol 3-kinase (PI3K) pathway. We and others have shown that PI3K, through activation of protein kinase B/Akt, inhibits transcriptional activation by a number of forkhead transcription factors (FoxO1, FoxO3, and FoxO4). In this study we have investigated the role of these forkhead transcription factors in the IL-2-induced T cell proliferation and survival. We show that IL-2 regulates phosphorylation of FoxO3 in a PI3K-dependent fashion. Phosphorylation and inactivation of FoxO3 appears to play an important role in IL-2-mediated T cell survival, because mere activation of FoxO3 is sufficient to trigger apoptosis in T cells. Indeed, active FoxO3 can induce expression of IL-2-regulated genes, such as the cdk inhibitor p27Kip1 and the proapoptotic Bcl-2 family member Bim. Furthermore, we show that IL-2 triggers a rapid, PI3K-dependent, phosphorylation of FoxO1a in primary T cells. Thus, we propose that inactivation of FoxO transcription factors by IL-2 plays a critical role in T cell proliferation and survival.
APTIMA assay on SurePath liquid-based cervical samples compared to endocervical swab samples facilitated by a real time database

Background: Liquid-based cytology (LBC) cervical samples are increasingly being used to test for pathogens, including: HPV, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) using nucleic acid amplification tests. Several reports have shown the accuracy of such testing on ThinPrep (TP) LBC samples. Fewer studies have evaluated SurePath (SP) LBC samples, which utilize a different specimen preservative. This study was undertaken to assess the performance of the Aptima Combo 2 Assay (AC2) for CT and GC on SP versus endocervical swab samples in our laboratory. Materials and Methods: The live pathology database of Montefiore Medical Center was searched for patients with AC2 endocervical swab specimens and SP Paps taken the same day. SP samples from CT-and/or GC-positive endocervical swab patients and randomly selected negative patients were studied. In each case, 1.5 ml of the residual SP vial sample, which was in SP preservative and stored at room temperature, was transferred within seven days of collection to APTIMA specimen transfer tubes without any sample or patient identifiers. Blind testing with the AC2 assay was performed on the Tigris DTS System (Gen-probe, San Diego, CA). Finalized SP results were compared with the previously reported endocervical swab results for the entire group and separately for patients 25 years and younger and patients over 25 years. Results: SP specimens from 300 patients were tested. This included 181 swab CT-positive, 12 swab GC-positive, 7 CT and GC positive and 100 randomly selected swab CT and GC negative patients. Using the endocervical swab results as the patient’s infection status, AC2 assay of the SP samples showed: CT sensitivity 89.3%, CT specificity 100.0%; GC sensitivity and specificity 100.0%. CT sensitivity for patients 25 years or younger was 93.1%, versus 80.7% for patients over 25 years, a statistically significant difference (P = 0.02). Conclusions: Our results show that AC2 assay of 1.5 ml SP samples transferred to APTIMA specimen transfer medium within seven days is sufficiently sensitive and specific to be used to screen for CT and GC. CT sensitivity may be somewhat reduced in samples from patients over 25 years. SP specimens retained in the original SP fixative for longer time intervals also may have decreased sensitivity, due to deterioration of RNA, but this was not assessed in this study. The ability to tap the live pathology database is a valuable tool that can useful to conduct clinical studies without a costly prospective clinical trial.
Cell‐bound exopolysaccharide from probiotic bacteria induces autophagic cell death of tumour cells

Aim: Lactic acid bacteria (LAB) are beneficial micro‐organisms that have been associated with several probiotic effects in both humans and animals. Here, using proteome analysis, we investigate the antitumour effects of cell‐bound exopolysaccharides (cb‐EPS) isolated from Lactobacillus acidophilus 606 on colon cancer cells and explore the proteins critical for their antitumour activity.
Can betaine partially replace or enhance the effect of methionine by improving broiler growth and carcase characteristics?

1. Growth rates and carcase characteristics were measured in male broiler chickens fed on a control diet deficient in methionine (c. 2·8 g/kg methionine) or a series of diets containing graded levels of betaine or DL-methionine or both additives. 2. We aimed to answer 2 main questions. First, can betaine replace part of the methionine in a broiler ration? Secondly, is there a synergism between methionine and betaine? 3. Birds given the control diet or that supplemented only with betaine ate less, grew more slowly, had higher food convension ratio (FCR) and varied more in mass at 42 d than birds fed diets with DL-methionine. Adding 1·2 g/kg DL-methionine to the control ration produced the heaviest birds at 42 d (2500 g) with the 2nd heaviest breast muscle (366 g). 4. After correcting for treatment differences in body mass (analysis of convariance), birds fed on the control diet and the diet supplemented with betaine only, had relatively lighter breast muscles but relatively heavier abdominal fat pads than those of birds given diets supplemented with DL-methionine. However, adding betaine to diets containing added methionine further improved the relative breast muscle yield. 5. After correcting for differences in body mass between treatments, birds fed on diets containing most methionine had lighter viscera than birds fed diets deficient in methionine. This demonstrated gut plasticity, suggesting that the viscera enlarged to sequester methionine from low-methionine diets. 6. Our data refute the hypothesis that betaine can substitute for methionine in broilers fed diets that are marginally deficient in methionine plus cystine. However, betaine may improve carcase composition, especially breast meat yield.
Results of laser in situ keratomileusis for myopia of -10 to -19 diopters with a Technolas 217 laser.

PURPOSE To evaluate the effectiveness, predictability, and safety of laser in situ keratomileusis (LASIK) for correcting myopia greater than -10.00 D. METHODS Sixty-five eyes of 37 patients with myopia greater than -10.00 D underwent LASIK. Patients were evaluated on day 1, 1 week, 1, 3, and 6 months after surgery. Parameters evaluated were uncorrected visual acuity (UCVA) and best spectacle-corrected visual acuity (BSCVA), residual refractive error, regression of correction, and presence of any complication. RESULTS Mean preoperative BSCVA was 0.745 +/- 0.234, which improved to 0.8070 +/- 0.237 postoperatively. The average preoperative UCVA was 0.022 +/- 0.02; postoperative UCVA at 6 months was 0.536 +/- 0.255. UCVA of 20/40 or better was achieved in 58% (38 eyes) and 20/20 or better in 26% (17 eyes). The average refractive error before LASIK was -12.64 +/- 2.16 D (range -10.00 to -19.00 D). Mean residual refractive error 1 week following LASIK was -0.63 +/- 1.36 D, which regressed to a mean -1.78 +/- 2.08 D at the end of 6 months. Nineteen eyes (29%) were within +/-0.50 D of intended refractive correction. CONCLUSION LASIK was partially effective in the correction of high myopia. An initial overcorrection may be programmed to offset the effect of refractive regression.
p38MAPK is involved in apoptosis development in apheresis platelet concentrates after riboflavin and ultraviolet light treatment

Pathogen inactivation (PI) accelerates the platelet (PLT) storage lesion, including apoptotic‐like changes. Proteomic studies have shown that phosphorylation levels of several kinases increase in PLTs after riboflavin and UV light (RF‐PI) treatment. Inhibition of p38MAPK improved in vitro PLT quality, but the biochemical basis of this kinase's contribution to PLT damage requires further analysis.
Adherence to oral therapies in pelvic inflammatory disease.

PURPOSE To assess adherence to oral therapies in pelvic inflammatory disease (PID). METHODS Medication adherence to oral doxycycline therapy (100 mg) was measured using electronic event monitoring (EEM) among adult women with PID. Subjects (n = 91), who were predominantly black and with a high school or lower educational attainment, were randomly selected from the Pelvic Inflammatory Disease Evaluation and Clinical Health (PEACH) Study, a trial in which subjects were randomized to either (1). initial inpatient then outpatient or (2). fully outpatient treatment with doxycycline and cefoxitin. Summary statistics calculated within treatment groups and in the cohort as a whole included the percentage of administrations taken, percentage of days with correct dosage, percentage of days with no drug taken, time elapsed until the first drug holiday, and percentage of optimal dosing intervals. RESULTS Study subjects took an average of 70% of prescribed doses, took the prescribed two daily doses for less than half of their outpatient days, took an unscheduled drug holiday for almost 25% of their outpatient days, and took only 16.9% of their doses within the optimal timing interval. In general, working, not bleeding with sex, and not drinking hard liquor were positively associated with measures of adherence. Adherence estimates were similar among women in the inpatient and outpatient groups after hospital discharge. CONCLUSIONS The disturbing rates of time interval adherence, even after hospitalization, suggest the need to determine the effectiveness of antibiotic regimens involving shorter courses and longer dosing intervals.
Pneumococcal Neuraminidases A and B Both Have Essential Roles during Infection of the Respiratory Tract and Sepsis

ABSTRACT We examined the role of the neuraminidases NanA and NanB in colonization and infection in the upper and lower respiratory tract by Streptococcus pneumoniae, as well as the role of these neuraminidases in the onset and development of septicemia following both intranasal and intravenous infection. We demonstrated for the first time using outbred MF1 mouse models of infection that both NanA and NanB were essential for the successful colonization and infection of the upper and lower respiratory tract, respectively, as well as pneumococcal survival in nonmucosal sites, such as the blood. Our studies have shown that in vivo a neuraminidase A mutant is cleared from the nasopharynx, trachea, and lungs within 12 h postinfection, while a neuraminidase B mutant persists but does not increase in either the nasopharynx, trachea, or lungs. We also demonstrated both neuraminidase mutants were unable to cause sepsis following intranasal infections. When administered intravenously, however, both mutants survived initially but were unable to persist in the blood beyond 48 h postinfection and were progressively cleared. The work presented here demonstrates the importance of pneumococcal neuraminidase A and for the first time neuraminidase B in the development of upper and lower respiratory tract infection and sepsis.