Miracle-dz/UniFAR-FTUs huggingface dataset:
Meat, fish, and ovarian cancer risk: Results from 2 Australian case-control studies, a systematic review, and meta-analysis.

BACKGROUND Variation in meat and fish intakes has been associated with a risk of some cancers, but evidence for ovarian cancer is limited and inconsistent. OBJECTIVE We examined the association between intakes of total meat, red meat, processed meat, poultry, and fish and ovarian cancer risk. DESIGN Data came from 2 Australian population-based case-control studies conducted 10 y apart. Analyses included a total of 2049 cases and 2191 control subjects. We obtained dietary information via a food-frequency questionnaire. We estimated multivariable-adjusted odds ratios (ORs) for each study by using logistic regression and combined results of the 2 studies by using random-effects models. We also assembled the published evidence in a systematic review and meta-analysis. RESULTS Although there was no association between total or red meat intake and ovarian cancer risk, women with the highest intake of processed meat had a significantly increased risk of ovarian cancer in the 2 case-control studies (combined OR: 1.18; 95% CI: 1.15, 1.21) and the meta-analysis [7 studies; pooled relative risk (RR): 1.20; 95% CI: 1.07, 1.34]. In contrast, a frequent intake of poultry was associated with borderline significant reductions in risk in the 2 case-control studies (combined OR: 0.83; 95% CI: 0.67, 1.03) and the meta-analysis including 7 additional studies (pooled RR: 0.90; 95% CI: 0.79, 1.01). High fish intake was associated with a significantly reduced risk in the 2 case-control studies (combined OR: 0.76; 95% CI: 0.62, 0.94) and a smaller borderline significant reduction in the meta-analysis (6 additional studies; pooled RR: 0.84; 95% CI: 0.68, 1.03). CONCLUSION Our results suggest that low consumption of processed meat and higher consumption of poultry and fish may reduce the risk of ovarian cancer.
Peptide nutrient‐energy dense enteral feeding in critically ill infants: an observational study

BACKGROUND Enteral feeding is challenging in critically ill infants. Target intakes are often not achieved as a result of fluid restriction, procedural interruptions and perceived enteral feeding intolerance. In those infants perceived to have poor feeding tolerance, the use of a peptide nutrient-energy dense enteral feed (PEF) may improve nutritional intake and minimise feeding interruptions as a result of gastrointestinal symptoms. The aim of this observational study was to characterise the use of a PEF amongst critically ill infants in two paediatric intensive care units (PICUs). METHODS Records from critically ill infants aged <12 months admitted to two PICUs were retrospectively reviewed with a PICU length of stay (LOS) ≥ 7 days. Achievement of nutritional targets for the duration of PEF was reviewed. Gastrointestinal symptoms, including gastric residual volume, constipation and vomiting, were evaluated as tolerance parameters. RESULTS In total, 53 infants were included, with a median age on admission of 2.6 months. Median admission weight was 3.9 kg in PICU-1 and 4.7 kg in PICU-2. Median (interquatile range) energy intake in PICU-1 and PICU-2 was 68 (47-92) and 90 (63-124) kcal kg-1 , respectively, and median (interquatile range) protein intake 1.7 (1.1-2.4) g kg-1 and 2.5 (1.6-3.2) g kg-1 , respectively. Feeding was withheld because of feeding intolerance in one infant (4%) on two occasions in PICU-1 for 2.5 h and in two infants (7%) on two occasions in PICU-2 for 19.5 h. Gastric residual mean (SD) volumes were 3.5 (5.4) mL kg-1 in PICU-1 and 16.9 (15.6) mL kg-1 in PICU-2. CONCLUSIONS Peptide nutrient-energy dense feeding in infants admitted to the PICU is feasible, well tolerated and nutritional targets are met. However, with this study design, it is not possible to draw any conclusions regarding the benefit of PEF over standard PE feed in critically ill children and future work is required to clarify this further.
Cervical Screening Results Leading to Detection of Adenocarcinoma in Situ of the Uterine Cervix

Background: Adenocarcinoma in situ (AIS) of the uterine cervix is a preinvasive lesion of the invasive adenocarcinoma. We analyzed the cervical screening results leading to detecting the AIS lesions including the co-existence of AIS lesions with high-grade squamous intra-epithelial lesions (HSIL) and invasive carcinoma. Methods: Women who were diagnosed and received treatment for AIS at Chiang Mai University Hospital between January 1, 2007 and August 31, 2016 were retrospectively reviewed. The inclusion criteria were the women who had pathological diagnosis of AIS obtained from cervical punch biopsy or excisional cone biopsy with either loop electrosurgical excision procedure (LEEP) or cold-knife conization (CKC). The patient characteristics, diagnostic work-up and treatment details were reviewed, including the cervical screening results prior to the diagnosis of cervical AIS, pathologic results of excisional cone biopsy and hysterectomy specimens. Results: During the study period, 75 women with AIS pathology undergoing excisional cone biopsy with either LEEP (n=62) or CKC (n=13) were identified. The abnormal cytologic screening leading to detection of AIS was the squamous cell abnormality accounting for 57.3%. Abnormal glandular cytology accounted for 37.3%. The most common abnormal cervical screening results was HSIL cytology (n = 25) followed by AIS cytology (n = 13). Normal cytology was noted in 4 women in whom 3 were positive for HPV 18 and 1 had AIS on the endocervical polyp. AIS coexisted with HSIL and invasive carcinoma were detected in cone biopsy specimens in 21 (28%) and 29 (38.7%) patients, respectively. Conclusion: The majority of cervical screening results leading to detection of cervical AIS was the squamous cell abnormality accounting for 57.3% in which, HSIL cytology was the most common. Abnormal glandular cytology accounted for only 37.3%. Diagnostic cone excision is recommended if AIS lesion is noted in cervical biopsy specimen since nearly 40% have coexisting invasive lesions.
Efficacy and Safety of Complete Intraureteral Stent Placement versus Conventional Stent Placement in Relieving Ureteral Stent Related Symptoms: A Randomized, Prospective, Single Blind, Multicenter Clinical Trial.

PURPOSE We compared the efficacy and safety of complete and conventional stent placement to relieve ureteral stent related symptoms. MATERIALS AND METHODS We randomized 85 patients who required ureteral stent placement after lithotripsy into an intraureteral or a conventional stent placement group. The ureteral stent remained in place until postoperative day 14. We evaluated scores on the visual analog scale pain, the SF-36 (36-Item Short-Form Health Survey), the I-PSS (International Prostate Symptom Score) and the OABSS (Overactive Bladder Symptom Score) on postoperative days 3 and 14. We also assessed the total amount of analgesics administered and stent related complications. RESULTS Overall the records of 80 patients were analyzed. Pain scores were significantly lower in the intraureteral vs the conventional stent placement group (postoperative days 3 and 14, 4.85 vs 9.78, p = 0.003, and 3.15 vs 6.20, p = 0.014, respectively). The total I-PSS score (postoperative days 3 and 14, 10.41 vs 14.90, p = 0.006, and 11.67 vs 16.10, p = 0.022, respectively) and total analgesic use (19.23 vs 88.54 mg, p <0.001) were significantly lower in the intraureteral group. However, differences in the SF-36 and the total OABSS scores did not significantly differ. On subgroup analysis the pain score in the groin and bladder areas, incomplete emptying and daytime frequency on the I-PSS, the quality of life index and daytime frequency on the OABSS were significantly better in the intraureteral stent placement group than the conventional stent placement group on postoperative days 3 and 14 (all p <0.05). There was no difference in the complication rate between the 2 groups. CONCLUSIONS Intraureteral stent placement may be associated with less ureteral stent related discomfort than conventional stent placement. This novel placement method is feasible and safe, and it can be immediately used in daily clinical practice.
Differential effects of alliance and techniques on Panic-Specific Reflective Function and misinterpretation of bodily sensations in two treatments for panic

ABSTRACT Objective: To examine whether working alliance quality and use of techniques predict improvement in Panic-Specific Reflection Function (PSRF), and misinterpretation of bodily sensations in treatments for panic disorder. Method: A sample of 161 patients received either CBT or PFPP (Panic-focused Psychodynamic therapy) within a larger RCT. Data were collected on patient-reported working alliance, misinterpretations, PSRF, observer-coded use of techniques, and interviewer-rated panic severity. Random-Intercept Cross-Lagged Panel Models assessed bi-directional associations, disentangling within- and between-patient effects, and accounting for prior change. Results: Higher alliance predicted subsequent within-patient improvement in PSRF in PFPP, but worsening in CBT. In both treatments, focus on interpersonal relationships predicted PRSF improvement (with stronger effects in CBT), while focus on thoughts and behaviors predicted worsening in PSRF. In CBT only, early focus on affect and moment-to-moment experience predicted reduced misinterpretation, while high focus on thoughts and cognitions predicted subsequent increase in misinterpretation. Conclusion: The quality of the alliance has differential effects on PSRF in distinct treatments. Interpersonal, rather than cognitive or behavioral focus, even when delivered differently within distinct treatments with high adherence, could facilitate improvement in PSRF. Additionally, early focus on affect and moment-to-moment experiences in CBT could reduce misinterpretations.
Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction

Significant efforts in wet and dry laboratories are devoted to resolving molecular structures. In particular, computational methods can now compute thousands of tertiary structures that populate the structure space of a protein molecule of interest. These advances are now allowing us to turn our attention to analysis methodologies that are able to organize the computed structures in order to highlight functionally relevant structural states. In this paper, we propose a methodology that leverages community detection methods, designed originally to detect communities in social networks, to organize computationally probed protein structure spaces. We report a principled comparison of such methods along several metrics on proteins of diverse folds and lengths. We present a rigorous evaluation in the context of decoy selection in template-free protein structure prediction. The results make the case that network-based community detection methods warrant further investigation to advance analysis of protein structure spaces for automated selection of functionally relevant structures.
Efficacy of food fortification on serum 25-hydroxyvitamin D concentrations: systematic review.

BACKGROUND Many residents of the United States and Canada depend on dietary sources of vitamin D to help maintain vitamin D status. Because few natural food sources contain vitamin D, fortified foods may be required. OBJECTIVE We aimed to determine the effects of vitamin D-fortified foods on serum 25-hydroxyvitamin D [25(OH)D] concentrations. DESIGN We searched MEDLINE (1966 to June Week 3 2006), Embase, CINAHL, AMED, Biological Abstracts, and the Cochrane Central Register of Controlled Trials for randomized controlled trials (RCTs) comparing vitamin D-fortified foods with a control and reporting serum 25(OH)D concentrations. Two reviewers independently determined study eligibility, assessed trial quality, and extracted relevant data. Disagreements were resolved by consensus. Meta-analyses of absolute mean change in 25(OH)D were conducted by using a random-effects model, with evaluation of heterogeneity. RESULTS Nine RCTs (n = 889 subjects) were included, of which 8 consistently showed a significant beneficial effect of food fortification on 25(OH)D concentrations. Although 7 RCTs (n = 585 subjects) potentially were meta-analyzable, we were unable to combine the overall results because of significant heterogeneity. The individual treatment effects ranged from 14.5 (95% CIs: 10.6, 18.4) nmol/L to 34.5 (17.64, 51.36) nmol/L (3.4-25 microg vitamin D/d). Subgroup analyses showed a reduction in heterogeneity and significant treatment effect when 4 trials that used milk as the fortified food source were combined. CONCLUSION Most trials were small in size and inadequately reported allocation concealment, but results showed that vitamin D-fortified foods improved vitamin D status in adults.
Multi-Steps Fragmentation-Ion Trap Mass Spectrometry Coupled to Liquid Chromatography Diode Array System for Investigation of Olaparib Related Substances

A high-performance liquid chromatography-diode array-mass spectrometric (LC-DAD-MS) method was developed and validated to investigate the related substances of olaparib (OLA) in bulk form. OLA was exposed to acid–base hydrolysis, boiling, oxidation with hydrogen peroxide, and UV light followed by LC-DAD-MS analysis. OLA and OLA-related substances were simultaneously and quantitatively monitored by DAD at 278 nm and triple quadrupole mass spectrometry (QQQ-MS). The investigated compounds were auto-scanned by an ion trap MS which applied positive and negative modes separately. The fragmentation pathway was confirmed by applying multi-steps fragmentation to identify the resulted cleaved ions and their parent ion. OLA was found to be sensitive to the alkaline hydrolysis and less sensitive to UV light. Two major hydrolytic degradation products, including the protonated molar ions m/z 299 and m/z 367, were identified. Three potential impurities were also characterized. The LC-MS limit of detection (LOD) and limit of quantification (LOQ) were 0.01 and 0.05 ng/µL, respectively. The quantitative results obtained by LC-DAD was comparable with that of LC-QQQ-MS. The proposed method shows good intra-day and inter-day precision with relative standard deviation (RSD) <2%.
The Use of Bone Morphogenetic Protein in the Intervertebral Disk Space in Minimally Invasive Transforaminal Lumbar Interbody Fusion

Study Design: Retrospective Cohort. Objective: The objective of this study was to characterize one surgeon’s experience over a 10-year period using rhBMP-2 in the disk space for minimally invasive transforaminal lumbar interbody fusion (MIS TLIF). Summary of Background Data: MIS TLIF has been utilized as a technique for decreasing patients’ immediate postoperative pain, decreasing blood loss, and shortened hospital stays. Effectiveness and complications of rhBMP-2’s use in the disk space is limited because of its off-label status. Methods: Retrospective analysis of consecutive MIS TLIFs performed by senior author between 2004 and 2014. rhBMP-2 was used in the disk space in all cases. Patients were stratified based on the dose of rhBMP-2 utilized. Patients had 9 to 12 month computerized tomography scan to evaluate for bony fusion and continued follow-up for 18 months. Results: A total of 688 patients underwent a MIS TLIF. A medium kit of rhBMP-2 was utilized in 97 patients, and small kit was used in 591 patients. Fusion rate was 97.9% and this was not different between the 2 groups with 96/97 patients fusing in the medium kit group and 577/591 patients fusing in the small kit group. Five patients taken back to the operating room for symptomatic pseudoarthrosis, 4 reoperated for bony hyperostosis, and 10 radiographic pseudoarthroses that did not require reoperation. A statistically significant difference in the rate of foraminal hyperostosis was found when using a medium sized kit of rhBMP-2 was 4.12% (4/97 patients), compared with a small kit (0/591 patients, P=0.0004). Conclusions: Utilization of rhBMP-2 in an MIS TLIF leads to high fusion rate (97.9%), with an acceptable complication profile. The development of foraminal hyperostosis is a rare complication that only affected 0.6% of patients, and seems to be a dose related complication, as this complication was eliminated when a lower dose of rhBMP-2 was utilized. Level of Evidence: Level IV.
Lexical competition during second-language listening: sentence context, but not proficiency, constrains interference from the native lexicon.

A spoken language eye-tracking methodology was used to evaluate the effects of sentence context and proficiency on parallel language activation during spoken language comprehension. Nonnative speakers with varying proficiency levels viewed visual displays while listening to French sentences (e.g., Marie va décrire la poule [Marie will describe the chicken]). Displays depicted several objects including the final noun target (chicken) and an interlingual near-homophone (e.g., pool) whose name in English is phonologically similar to the French target (poule). Listeners' eye movements reflected temporary consideration of the interlingual competitor when hearing the target noun, demonstrating cross-language lexical competition. However, competitor fixations were dramatically reduced when prior sentence information was incompatible with the competitor (e.g., Marie va nourrir. [Marie will feed.]). In contrast, interlingual competition from English did not vary according to participants' rated proficiency in French, even though proficiency reliably predicted other aspects of processing behavior, suggesting higher proficiency in the active language does not provide a significant independent source of control over interlingual competition. The results provide new insights into the nature of parallel language activation in naturalistic sentential contexts.
A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data

Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.
Combined Testing of p16 Tumour-suppressor Protein and Human Papillomavirus in Patients With Oral Leukoplakia and Oral Squamous Cell Carcinoma

Background: Oral leukoplakia (OL) is a potentially malignant oral mucosal disorder. A casual association between OL, oral squamous cell carcinoma (OSCC) and human papillomavirus (HPV) infection has been suggested, but no conclusive evidence has been presented. p16, a tumour-suppressor protein, is used as a surrogate marker for HPV infection. The aim of this study was to investigate how overexpression of p16 correlates with HPV infection in OL and in OSCC. Patients and Methods: Seventy-four patients with OL and 13 with OSCC with p16 overexpressed, were analyzed by immunohistochemistry visualizing p16 and a real-time polymerase chain reaction (PCR) assay targeting HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 52, 56, 58 and 59. Results: Overexpression of p16 was observed in 18% of patients with OL. None of the HPV subtypes were detected by PCR analysis in patients with OL. In the p16-positive OSCC specimens, 38% were also HPV16-positive. Conclusion: Overexpression of p16 was not found to be a reliable biomarker for HPV infection in patients with OL and OSCC.
Pulse and vital sign measurement in mixed reality using a HoloLens

Cardiography, quantitative measurement of the functioning of the heart, traditionally requires customized obtrusive contact sensors. Using new methods photoplethysmography and ballistocardiography signals can be captured using ubiquitous sensors, such as webcams and accelerometers. However, these signals are not visible to the unaided eye. We present Cardiolens - a mixed reality system that enables real-time, hands-free measurement and visualization of blood flow and vital signs from multiple people. The system combines a front-facing webcam, imaging ballistocardiography, and remote imaging photoplethysmography methods for recovering pulse signals. A heads up display allows users to view their own heart rate whenever they are wearing the device and the heart rate and heart rate variability of another person simply by looking at them. Cardiolens provides the wearer with a new way to understand physiological signals and has applications in human-computer interaction and in the study of social psychology.
Origin of Cardiac Troponin T Elevations in Chronic Kidney Disease.

Plasma concentrations of cardiac troponins, the preferred biomarkers for the diagnosis of acute myocardial infarction, are often persistently elevated in patients with chronic kidney disease (CKD). The origin of these elevations is unknown: Is it the heart, by increased release, or the kidneys, by decreased renal elimination? In clinical practice, this equivocal view on troponin elevations in patients with reduced glomerular clearance underlies countless clinical discussions among physicians and may delay rapid initiation of adequate treatment when these patients present with chest pain. In the present study, we aimed to discriminate between increased cardiac release and reduced renal elimination as the main process underlying this phenomenon. Specifically, we used the recently demonstrated rhythmic diurnal oscillation pattern of troponin T as a model to assess the contribution of impaired renal elimination to persistently elevated cardiac troponin levels in patients with CKD.1 The diurnal troponin T rhythm is characterized by gradually decreasing concentrations throughout daytime and rising concentrations during nighttime.1 If decreased renal clearance, and not increased production, is the key driver of elevated troponins in patients with CKD, the increased half-life and subsequent accumulation of cardiac troponin T will fade its diurnal rhythm. …