Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring and accounting for publication bias in mental health: a brief overview of methods

Objective Publication bias undermines the integrity of published research. The aim of this paper is to present a synopsis of methods for exploring and accounting for publication bias. Methods We discussed the main features of the following methods to assess publication bias: funnel plot analysis; trim-and-fill methods; regression techniques and selection models. We applied these methods to a well-known example of antidepressants trials that compared trials submitted to the Food and Drug Administration (FDA) for regulatory approval. Results The funnel plot-related methods (visual inspection, trim-and-fill, regression models) revealed an association between effect size and SE. Contours of statistical significance showed that asymmetry in the funnel plot is probably due to publication bias. Selection model found a significant correlation between effect size and propensity for publication. Conclusions Researchers should always consider the possible impact of publication bias. Funnel plot-related methods should be seen as a means of examining for small-study effects and not be directly equated with publication bias. Possible causes for funnel plot asymmetry should be explored. Contours of statistical significance may help disentangle whether asymmetry in a funnel plot is caused by publication bias or not. Selection models, although underused, could be useful resource when publication bias and heterogeneity are suspected because they address directly the problem of publication bias and not that of small-study effects.
Adaptedness and heterosis in corn and mule hybrids

The origin of U.S. Corn Belt corn (Zea mays L.), heterotic groups, and heterotic patterns becomes less obvious with more cycles of breeding. Heterosis is poorly understood; simple curiosity cries out for more information. I endeavor to shed light on the effect of adaptedness and heterosis on U.S. Corn Belt corn. I relate pertinent happenings in the phenomenal increase in U.S. corn production. I briefly review the origins of Northern Flint and Southern Dent races of corn and two major, persistent open-pollinated cultivars; and how corn hybridization was preceded and eased by hybrid species of the horse (Equus spp.). I discuss heterotic groups and patterns. The objective of U.S. corn breeding has been to adapt a tropical crop to a temperate climate. Adaptedness is important. Open-pollinated cultivars emphasized local adaptation, but some cultivars were more popular, widely grown, and better adapted over a broad geographic region. Hybrid seed corn companies grew larger by selling more widely adapted hybrids that favored germplasm from the more popular, widely grown, better adapted open-pollinated cultivars containing more genes for adaptedness. I examine morphological differences between inbred parents of a widely adapted hybrid. Relatively constant percentage of heterosis of well-adapted hybrids over years is due to seasonal climate affecting hybrids and their parent inbreds in a like manner because of their selection for adaptedness. Adaptedness has been more important than heterosis in the U.S. corn yield and production increases. Adaptedness in analogous heterotic species hybrids of the genus Equus, where body size is female dominant, apparently discriminates for body size between mules and hinnies that have virtually identical genotypes—adaptedness determines superiority over and above heterosis.
The association between race and attitudes about predictive genetic testing.

OBJECTIVES To investigate differences in attitudes about predictive genetic testing for cancer risk between African-American and Caucasian residents of the city of Philadelphia. METHODS Cross-sectional survey of awareness of and attitudes about predictive genetic testing, using an instrument developed through focus groups with the general public, literature review, and expert opinion. SETTING Municipal County Courthouse of Philadelphia. RESPONDENTS Male and female adults waiting to be assigned to jury duty. RESULTS Of the 430 respondents, 43% (170) were African-American and 45% (181) Caucasian. Awareness of predictive genetic testing was higher among Caucasians (72%) than African-Americans (49%). After adjustment for age, gender, and educational attainment, African-Americans were more likely to report that the government would use genetic tests to label groups as inferior, and less likely to endorse the potential health benefits of testing, including "help my doctor manage my health care," "help me change my lifestyle," and "help scientists find cures for diseases. " These associations remained if the sample was restricted to participants who had heard of genetic testing before the survey. CONCLUSIONS In the city of Philadelphia, awareness of and attitudes about predictive genetic testing for cancer risk differ by race, with lower awareness, less belief in the potential benefits of testing, and more concern about racial discrimination from genetic testing among African-Americans than Caucasians. These differences may result in disparities in the uptake of predictive genetic testing in the future.
The clinical course of advanced dementia.

BACKGROUND Dementia is a leading cause of death in the United States but is underrecognized as a terminal illness. The clinical course of nursing home residents with advanced dementia has not been well described. METHODS We followed 323 nursing home residents with advanced dementia and their health care proxies for 18 months in 22 nursing homes. Data were collected to characterize the residents' survival, clinical complications, symptoms, and treatments and to determine the proxies' understanding of the residents' prognosis and the clinical complications expected in patients with advanced dementia. RESULTS Over a period of 18 months, 54.8% of the residents died. The probability of pneumonia was 41.1%; a febrile episode, 52.6%; and an eating problem, 85.8%. After adjustment for age, sex, and disease duration, the 6-month mortality rate for residents who had pneumonia was 46.7%; a febrile episode, 44.5%; and an eating problem, 38.6%. Distressing symptoms, including dyspnea (46.0%) and pain (39.1%), were common. In the last 3 months of life, 40.7% of residents underwent at least one burdensome intervention (hospitalization, emergency room visit, parenteral therapy, or tube feeding). Residents whose proxies had an understanding of the poor prognosis and clinical complications expected in advanced dementia were much less likely to have burdensome interventions in the last 3 months of life than were residents whose proxies did not have this understanding (adjusted odds ratio, 0.12; 95% confidence interval, 0.04 to 0.37). CONCLUSIONS Pneumonia, febrile episodes, and eating problems are frequent complications in patients with advanced dementia, and these complications are associated with high 6-month mortality rates. Distressing symptoms and burdensome interventions are also common among such patients. Patients with health care proxies who have an understanding of the prognosis and clinical course are likely to receive less aggressive care near the end of life.
Reduction of 4-nitroquinoline l-oxide by microorganisms.

The ultraviolet absorption maximum of 4-nitroquinoline 1-oxide was shifted toward shorter wave length when the substance was added to the growing media of microorganisms. The investigation of this phenomenon revealed that the shift in ultraviolet absorption maxima is due to the reduction of nitro group at 4-position. It was also foundthat the reduction of N→Obond in 1-position occurs to a smaller extent.
Ventilator-Associated Events: Prevalence, Outcome, and Relationship With Ventilator-Associated Pneumonia*

Objectives:Centers for Disease Control and Prevention built up new surveillance paradigms for the patients on mechanical ventilation and the ventilator-associated events, comprising ventilator-associated conditions and infection-related ventilator-associated complications. We assess 1) the current epidemiology of ventilator-associated event, 2) the relationship between ventilator-associated event and ventilator-associated pneumonia, and 3) the impact of ventilator-associated event on antimicrobials consumption and mechanical ventilation duration. Design:Inception cohort study from the longitudinal prospective French multicenter OUTCOMEREA database (1996-2012). Patients:Patients on mechanical ventilation for greater than or equal to 5 consecutive days were classified as to the presence of a ventilator-associated event episode, using slightly modified Centers for Disease Control and Prevention definitions. Intervention:None. Measurements and Main Results:Among the 3,028 patients, 2,331 patients (77%) had at least one ventilator-associated condition, and 869 patients (29%) had one infection-related ventilator-associated complication episode. Multiple causes, or the lack of identified cause, were frequent. The leading causes associated with ventilator-associated condition and infection-related ventilator-associated complication were nosocomial infections (27.3% and 43.8%), including ventilator-associated pneumonia (14.5% and 27.6%). Sensitivity and specificity of diagnosing ventilator-associated pneumonia were 0.92 and 0.28 for ventilator-associated condition and 0.67 and 0.75 for infection-related ventilator-associated complication, respectively. A good correlation was observed between ventilator-associated condition and infection-related ventilator-associated complication episodes, and ventilator-associated pneumonia occurrence: R2 = 0.69 and 0.82 (p < 0.0001). The median number of days alive without antibiotics and mechanical ventilation at day 28 was significantly higher in patients without any ventilator-associated event (p < 0.05). Ventilator-associated condition and infection-related ventilator-associated complication rates were closely correlated with antibiotic use within each ICU: R2 = 0.987 and 0.99, respectively (p < 0.0001). Conclusions:Ventilator-associated event is very common in a population at risk and more importantly highly related to antimicrobial consumption and may serve as surrogate quality indicator for improvement programs.
Thought disorder in childhood schizophrenia: replication and update of concept.

OBJECTIVES To examine whether measures of thought disorder differentiated schizophrenic from normal children and to examine the relationship of these measures with developmental and cognitive factors. METHOD The speech samples of 88 schizophrenic and 190 normal children, aged 9 to 13 years, were coded with the Kiddie Formal Thought Disorder Rating Scale and Halliday and Hassan's analysis of cohesion. RESULTS Above and beyond differences in mental age, gender, and neuroleptic status, the patients had significantly more formal thought disorder (FTD) and cohesive deficits than the normal children matched by mental age. The younger schizophrenic and normal children had significantly more thought disorder than the older children with these diagnoses. Combined FTD and cohesion scores correctly identified 76% of schizophrenic and 88% of normal children with little variability across mental age. The thought disorder measures generated 2 independent components: FTD and cohesion. CONCLUSIONS Thought disorder measures that include both FTD and cohesion provide a quantitative diagnostic tool of childhood-onset schizophrenia.
Out of Mind, Out of Sight

In the present study, the effect of memory suppression on subsequent perceptual processing of visual objects was examined within a modified think/no-think paradigm. Suppressing memories of visual objects significantly impaired subsequent perceptual identification of those objects when they were briefly encountered (Experiment 1) and when they were presented in noise (Experiment 2), relative to performance on baseline items for which participants did not undergo suppression training. However, in Experiment 3, when perceptual identification was performed on mirror-reversed images of to-be-suppressed objects, no impairment was observed. These findings, analogous to those showing forgetting of suppressed words in long-term memory, suggest that suppressing memories of visual objects might be mediated by direct inhibition of perceptual representations, which, in turn, impairs later perception of them. This study provides strong support for the role of inhibitory mechanisms in memory control and suggests a tight link between higher-order cognitive operations and perceptual processing.
The procedure of a camera calibration using Camera Calibration Toolbox for MATLAB

This paper describes the calibration procedure of a CCD digital camera based on the perspective projection method. The idea of this method is to calibrate the camera in order to extract precise three dimensional information from the images so that they can be used for the computer vision and similar applications which take the images acquired from the camera as an input. The image capturing process reduces the dimensions of data from three to two. The camera calibration procedure determines which light source is associated with each pixel on the resulting image. Since the camera used in the process is a complex CCD camera, errors resulting from the misaligned lenses and deformations in their structures result in more complex distortions in the acquired image. In order to associate the points in the cameras image space with the locations in a 3D world space the camera projection matrix consisting of the estimated intrinsic and extrinsic parametars is calculated. The calibration process is comprised of capturing calibration images and processing them in order to get the intrinsic and extrinsic camera parameters. The results of the calibration are tested using the test images captured with the same camera. The calibration process was implemented using a MATLAB software package.
Predictability of outcome of caustic ingestion by esophagogastroduodenoscopy in children.

AIM To assess the necessity of esophagogastroduodenoscopy (EGD) to predict the outcome of caustic ingestion in children. METHODS The study included 206 children who underwent EGD because of ingestion of caustic substances between January 2005 and August 2010. Retrospective analysis of data of the patients was performed. RESULTS The male/female ratio was 1.6 and mean age was 38.1 ± 28.8 mo. The caustic substances were acidic in 72 (34.9%) cases, alkaline in 56 (27.2%), liquid household bleach in 62 (30.1%), and unknown in 16 (7.8%). Fifty-seven (27.7%) patients were symptom-free. Significant clinical findings were observed in 149 (72.3%) patients. Upper gastrointestinal endoscopy findings of esophageal injury were grade 0 in 86 (41.7%) patients, grade 1 in 49 (23.8%), grade 2a in 42 (20.4%), grade 2b in 28 (13.6%), and grade 3a in 1 (0.5%) patient. 35 patients with grade 2a, 2b, and 3a injuries underwent esophageal dilation at second week of ingestion. Esophageal stricture, which necessitated a regular dilation program developed in 13 of the aforementioned 35 patients. There is no statistically significant difference in the rate of development of esophageal stricture between the patients who ingested acidic (15.3%) and alkaline (8.9%) substances (P = 0.32). Severe gastric injury was detected in 38 (18.5%) patients. The rate of development of gastric injury was significantly higher in the acidic group (14%) than in the alkaline group (2.9%) (P = 0.001). Out of 149 patients with clinical findings, 49 (32.9%) patients had no esophageal injury and 117 (78.5%) patients had no gastric lesion. Esophageal and severe gastric injuries were detected in 20 (35.1%) and 8 (14%) of patients with no clinical findings respectively. Pyloric stenosis developed in 6 patients. Pyloric obstruction improved with balloon dilation in 2 patients. Mean hospitalization time were 1.2 ± 0.5 d for grade 0 and 2.3 ± 5 d for grade 1 and 6.3 ± 6.2 d for grade 2a and 15.8 ± 18.6 d for grade 2b. It was significantly longer for patients with grade 2a and 2b injuries (P = 0.000). CONCLUSION Endoscopy is an effective technique for determining the presence of esophageal and gastric damage and to avoid unnecessary treatment in patients with no or mild injury.
Laparoscopic Placement of Tenckhoff Catheters for Peritoneal Dialysis: A Safe, Effective, and Reproducible Procedure

Background/Aims Currently there are several techniques for laparoscopic placement of peritoneal dialysis catheters. The aim of this paper is to describe our technique and outcomes. Patients and Methods Laparoscopic implantation of peritoneal catheters was performed in 100 consecutive patients. The technique employed laparoscopically guided mus-culofascial tunneling to maintain catheter orientation toward the deep pelvis, and adhesiolysis to eliminate compartmentalization that could affect completeness of dialysate drainage. Mean duration of surgery, hospital stay, morbidity, mortality, and catheter survival were assessed. Analysis of catheter survival was performed using the Kaplan–Meier method, with censoring of catheter loss due to death or successful transplantation. Results Mean operative time was 20 ± 7 minutes and average duration of hospital stay was 3 ± 1 days. There were no conversions from laparoscopy to conventional catheter insertion methods. No exit-site or tunnel infections, hemorrhagic complications, abdominal wall hernias, or catheter cuff extrusions were detected. No mortality occurred in this series of patients. Catheter survival was 97%, 95%, and 91% at 1, 2, and 3 years, respectively. Conclusions The laparoscopic method described in this report is compliant with consensus guidelines for best-demonstrated practices in peritoneal access placement. Laparoscopy permits direct visualization of all procedure steps in a safe efficient reproducible manner. The laparoscopic approach afforded patients the advantage of short procedure times, a minimally invasive approach, and excellent outcomes. The results reported in this paper support our opinion that laparoscopic Tenckhoff catheter implantation should become the standard of care for clinical practice.
Regulation of proline utilization in Salmonella typhimurium: characterization of put::Mu d(Ap, lac) operon fusions

The genes for proline utilization were fused to the structural genes of the lac operon by use of the hybrid Mu phage derivative Mu d(Ap lac). Stable deletion derivatives of these fusions were selected and used to study the transcriptional regulation of the put genes. Analysis of these fusions showed that the putA gene product, a bifunctional oxidase-dehydrogenase, also serves to negatively control transcription of the putA and putP genes. Transcription of the put genes is repressed only in putA+ strains; this repression is lifted when exogenous proline is supplied. Transcription of the put genes is stimulated by cyclic AMP in putA+ and putA strains. Maximal induction of the put genes in putA+ strains requires oxygen or an alternative electron acceptor. This oxygen effect is mediated by the putA protein since putA mutants show maximal transcription even without an electron acceptor. The orientation of the Mu d(Ap lac) insertions was determined by formation of Hfr's via the lac homology on F'ts114 lac+. The direction of chromosome mobilization by these Mu d(Ap lac)-directed Hfr's demonstrated that the putP and putA genes are divergently transcribed from a central regulatory region lying between them.
Hydroxymatairesinol, a Novel Enterolactone Precursor With Antitumor Properties From Coniferous Tree (Picea abies)

Abstract: The potential for the extraction of the plant lignan hydroxymatairesinol (HMR) in large scale from Norway spruce (Picea abies) has given us the opportunity to study the metabolism and biological actions of HMR in animals. HMR, the most abundant single component of spruce lignans, was metabolized to enterolactone (ENL) as the major metabolite in rats after oral administration. The amounts of urinary ENL increased with the dose of HMR (from 3 to 50 mg/kg), and only minor amounts of unmetabolized HMR isomers and other lignans were found in urine. HMR (15 mg/kg body wt po) given for 51 days decreased the number of growing tumors and increased the proportion of regressing and stabilized tumors in the rat dimethylbenz[a]anthracene-induced mammary tumor model. HMR (50 mg/kg body wt) did not exert estrogenic or antiestrogenic activity in the uterine growth test in immature rats. HMR also showed no antiandrogenic responses in the growth of accessory sex glands in adult male rats. Neither ENL nor enterodiol showed estrogenic or antiestrogenic activity via a classical a- or b-type estrogen receptor-mediated pathway in vitro at <1.0 mM. HMR was an effective antioxidant in vitro.
CTC-derived AR-V7 detection as a prognostic and predictive biomarker in advanced prostate cancer

ABSTRACT Introduction: Prostate cancer is a highly heterogeneous disease, with remarkably different prognosis across all stages. Increased circulating tumor cell (CTC) count (≥ 5) using the CellSearch assay has been identified as one of the markers that can be used to predict survival, with added value beyond currently available prognostic factors. Recently, androgen receptor splice variant 7 (AR-V7) detection has been associated with worse outcomes for patients with castration-resistant prostate cancer (CRPC) treated with novel androgen receptor-signaling (ARS) inhibitors such as abiraterone and enzalutamide but not taxane chemotherapies. Areas covered: In this manuscript, the authors review the available biomarkers in CRPC and discuss emerging data on the value of CTC-derived AR-V7 status to assess prognosis and its potential role to guide treatment selection for patients with advanced prostate cancer. Expert commentary: Current evidence supports AR-V7 status as a prognostic biomarker and also as a potential predictive biomarker for patients with mCRPC. The authors expect that the incorporation of AR-V7 status and other biomarkers (e.g. AR mutations) in the sequential assessment of patients with advanced prostate cancer will lead to a more rational use of available and future therapies, with significant improvements in outcomes for our patients.
Deterministic Convergence for Learning Control Systems Over Iteration-Dependent Tracking Intervals

This brief addresses the iterative learning control (ILC) problems for discrete-time systems subject to iteration-dependent tracking time intervals. A modified class of P-type ILC algorithms is proposed by properly defining an available modified output, for which robust convergence analysis is performed with an inductive approach. It is shown that if a persistent full-learning property is ensured, then a necessary and sufficient convergence condition of ILC can be derived to reach the perfect output tracking objective though the tracking time interval is iteration-dependent. That is, the tracking of ILC for iteration-dependent time intervals can be guaranteed in the same deterministic (not stochastic) convergence way as that of traditional ILC over a fixed time interval. Furthermore, the developed tracking results can be extended to admit iteration-dependent uncertainties in initial state and external disturbances. Simulation tests are also included to demonstrate the effectiveness of the modified P-type ILC.