Clear cell renal cell carcinoma with BAP1 mutation: a report of two cases.

Clear cell renal cell carcinoma is the most common subtype of renal cell carcinomas (RCCs) and accounts for 60%-70% of all RCCs cases in adults. Aberrations in the von Hippel-Lindau (VHL) gene on chromosome 3p occurred in > 90% of clear cell RCCs. Other tumor suppressor genes located on chromosome 3p, such as BAP1, PBRM1, and SETD2, also contribute to tumorigenesis. Clear cell RCCs with both BAP1 and VHL mutations may display distinctive histopathological features. Here, we report two cases of clear cell RCCs with BAP1 mutation. One tumor had VHL, BAP-1, and RAF1 mutations and the tumor nests and alveoli of tumor cells were surrounded by proliferative vessels and the optically clear cytoplasm contained numerous eosinophilic granules and hyaline globules of varying sizes. The other tumor had BAP1 and ATM mutations, and demonstrated clear cells with numerous eosinophilic granules and other typical histopathological features of conventional clear cell RCC. Furthermore, many tumor nodules with dense peripheral lymphocytic infiltrates contained rhabdoid cells. Sarcomatoid cells were also observed. Both tumor cells showed high-grade nuclei. Clear cell RCCs with BAP1 mutation exhibit aggressive clinical behaviors.

Sire pedigree error estimation and sire verification of the Taiwan dairy cattle population by using SNP markers.

Information regarding the correct pedigree of and relationship between animals is useful for managing dairy breeding, reducing inbreeding, estimating breeding value, and establishing correct breeding programs. Additionally, the successful implementation of progeny testing is crucial for improving the genetics of dairy cattle, which depends on the availability of correct pedigree information. Incorrect pedigree information leads to bias in bull evaluation. In this study, Neogen GeneSeek Genomic Profiler (GGP) 50K SNP chips were used to identify and verify the sire of Taiwanese Holstein dairy cattle and analyze the reasons that lead to incorrect sire records. Samples were collected from 2,059 cows of 36 dairy farms, and the pedigree information was provided by breeders. The results of sire verification can be divided into three categories: submitted unconfirmed sire, submitted confirmed sire, and incorrectly submitted verified sire. Data on the sires of 1,323 (64.25%) and 572 (27.78%) dairy cows were verified and discovered, respectively. Sires of 1,895 (92.03%) dairy cattle were identified, which showed that the paternal pedigree of dairy cattle could be discovered and verified through genetic testing. An error-like analysis revealed that the data of 37 sires were incorrectly recorded because the bull's NAAB code number was incorrectly entered into the insemination records: for 19 sires, the wrong bull was recorded because the frozen semen of a bull placed in the wrong storage tank was used, 6 had no sire records, and for 12 sires, the NAAB code of the correct bull was recorded but with a wrong stud code, marketing code, or unique number for the stud or breed. To reduce recorded sire error rates by at least 27.78%, automated identification of the mated bull must be adopted to reduce human error and improve dairy breeding management on dairy farms.

Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source.

Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS-WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV-Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS-WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005-2.0 Å-1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.

Social Well-Being, Psychological Factors, and Chronic Conditions Among Older Adults.

Background: Aging is characterized by the decline in physical health, functional status, and loss of social roles and relationships that can challenge the quality of life. Social well-being may help explain how aging individuals experience declining physical health and social relationships. Despite the high prevalence of chronic conditions among older adults, research exploring the relationship between social well-being and chronic disease is sparse. Objectives: The study aims were to investigate the relationship between social well-being and psychological factors (e.g., perceived control, life satisfaction, self-esteem, active coping, optimism, and religious coping) by chronic condition in older adults. Design: Cross-sectional study. Participants: The current study comprises older adults (N = 1,251, aged ≥ 65 y) who participated in the third wave of the National Survey of Midlife in the United States (i.e., MIDUS). Setting: MIDUS was conducted on a random-digit-dial sample of community-dwelling, English-speaking adults. Measurements: Six instruments representing psychological resources (life satisfaction, perceived control, self-esteem, optimism, active coping, and religious coping) and five dimensions of social well-being (social actualization, social coherence, social acceptance, social contribution, social integration) were measured. An index of chronic disease comprised of self-reported data whether they had received a physician's diagnosis for any chronic conditions over the past year. Results: The findings indicated that the individuals without chronic conditions had significantly higher social integration, social acceptance, and social contribution scores than the individuals with chronic conditions (t = 2.26, p < 0.05, t = 2.85, p < 0.01, and t = 2.23, p < 0.05, respectively). For individuals diagnosed with more than one chronic condition, perceived control, self-esteem, and optimism were positively related to their social well-being (ß = .33, p < .001, ß = .17, p < .001, and ß = .33, p < .001, respectively). Conclusion: Findings suggested that older adults with multiple chronic conditions have a decrease in social well-being. Chronic disease management programs may help increase social well-being among individuals with multiple chronic conditions.

Total knee replacement in osteoarthritis patients on reducing the risk of major adverse cardiac events: a 18-year retrospective cohort study.

OBJECTIVES: Osteoarthritis (OA) is a common degenerative joint disease, and total knee replacement (TKR) is a successful surgical intervention for knee OA treatment. However, the risks of mortality and major cardiovascular events (MACEs) in patients receiving TKR remain unclear. This study investigated the risks of mortality and MACEs in knee OA patients who received TKR. METHODS: For this population-based cohort study, the Longitudinal Health Insurance Database 2000 was used. Two million individuals with knee OA defined by ICD-9-CM codes who received physical therapy between 1999 and 2017 were selected. For propensity score matching (PSM), we considered the year of knee OA diagnosis, demographics, comorbidities, co-medications, and knee OA-related hyaluronic acid or physical therapy at baseline. After PSM, regression analyses were performed to assess the association of mortality or MACEs with TKR and non-TKR individuals. RESULTS: We identified patients (n = 189,708) with a new diagnosis of knee OA between 2000 and 2017. In total, 10,314 propensity-score-paired TKR and non-TKR individuals were selected. The PSM cohort algorithm revealed that the risk of mortality or MACEs was lower in the TKR group (adjusted hazard ratio: 0.791; 95% confidence interval: 0.755-0.830) than in the non-TKR group. CONCLUSIONS: Patients with knee OA who received TKR had decreased risks of mortality and MACEs than those who did not receive TKR. Moreover, the TKR group received a reduced dosage of nonsteroidal anti-inflammatory drugs at the 1-year follow-up.

Comparison of clinical outcomes of edoxaban versus apixaban, dabigatran, rivaroxaban, and vitamin K antagonists in patients with atrial fibrillation in Germany: A real-world cohort study.

BACKGROUND: The aim of the study was to compare the real-world effectiveness and safety in atrial fibrillation (AF) patients treated with edoxaban versus other oral anticoagulants (OACs) (apixaban, dabigatran, rivaroxaban, and vitamin K antagonists [VKA]) in Germany. METHODS AND RESULTS: Using a representative database of 3.5 million statutory health-insured lives in Germany, a retrospective cohort study was conducted to examine ischemic stroke (IS) or systemic embolism (SE) and major bleeding in AF patients initiating anticoagulant therapy from January 2014 through June 2017. Inverse probability of treatment weighting using propensity score was applied for baseline covariate adjustment. Cox proportional hazards models were used to estimate the adjusted risk (hazard ratio [HR]) of each outcome comparing edoxaban versus other OACs. Among 21,038 patients treated with OACs, 1236 edoxaban, 6053 apixaban, 1306 dabigatran, 7013 rivaroxaban, and 5430 VKA patients were included. The adjusted combined risks of IS or SE were lower (p < 0.05) for each edoxaban pairwise comparison with other OACs (HR: 0.83 vs. apixaban, 0.60 vs. dabigatran, 0.72 vs. rivaroxaban, 0.64 vs. VKA). Edoxaban favored lower risks of major bleeding compared with rivaroxaban (HR: 0.74) and VKA (HR: 0.47). No differences in the risk of major bleeding were found between edoxaban and apixaban (p = 0.33), and between edoxaban and dabigatran (p = 0.06). CONCLUSIONS: Edoxaban was associated with better effectiveness compared with other OACs in AF patients from Germany. Edoxaban also demonstrated a favorable safety profile.

Optical design and performance of the biological small-angle X-ray scattering beamline at the Taiwan Photon Source.

The optical design and performance of the recently opened 13A biological small-angle X-ray scattering (SAXS) beamline at the 3.0 GeV Taiwan Photon Source of the National Synchrotron Radiation Research Center are reported. The beamline is designed for studies of biological structures and kinetics in a wide range of length and time scales, from angstrom to micrometre and from microsecond to minutes. A 4 m IU24 undulator of the beamline provides high-flux X-rays in the energy range 4.0-23.0 keV. MoB4C double-multilayer and Si(111) double-crystal monochromators (DMM/DCM) are combined on the same rotating platform for a smooth rotation transition from a high-flux beam of ∼4 × 1014 photons s-1 to a high-energy-resolution beam of ΔE/E ≃ 1.5 × 10-4; both modes share a constant beam exit. With a set of Kirkpatrick-Baez (KB) mirrors, the X-ray beam is focused to the farthest SAXS detector position, 52 m from the source. A downstream four-bounce crystal collimator, comprising two sets of Si(311) double crystals arranged in a dispersive configuration, optionally collimate the DCM (vertically diffracted) beam in the horizontal direction for ultra-SAXS with a minimum scattering vector q down to 0.0004 Å-1, which allows resolving ordered d-spacing up to 1 µm. A microbeam, of 10-50 µm beam size, is tailored by a combined set of high-heat-load slits followed by micrometre-precision slits situated at the front-end 15.5 m position. The second set of KB mirrors then focus the beam to the 40 m sample position, with a demagnification ratio of ∼1.5. A detecting system comprising two in-vacuum X-ray pixel detectors is installed to perform synchronized small- and wide-angle X-ray scattering data collections. The observed beamline performance proves the feasibility of having compound features of high flux, microbeam and ultra-SAXS in one beamline.

Risk of Myocardial Infarction and Ischemic Stroke after Dental Treatments.

The association between invasive dental treatments (IDTs) and a short-term risk of myocardial infarction (MI) and ischemic stroke (IS) remains controversial. Bacterial dissemination from the oral cavity and systemic inflammation linked to IDT can induce a state of acute vascular dysfunction. The aim of study is to investigate the relation of IDTs to MI and IS by using case-only study designs to analyze data from a large Taiwanese cohort. A nationwide population-based study was undertaken by using the case-crossover and self-controlled case series design to analyze the Taiwanese National Health Care Claim database. Conditional logistic regression model and conditional Poisson regression model were used to estimate the risks of MI/IS. In addition, we used burn patients as negative controls to explore the potential effect of residual confounding. In total, 123,819 MI patients and 327,179 IS patients in the case-crossover design and 117,655 MI patients and 298,757 IS patients were included in the self-controlled case series design. Results from both study designs showed that the risk of MI within the first 24 wk after IDT was not significantly different from or close to unity except for a modest risk during the first week for patients without other comorbidities (odds ratios [95% confidence intervals] of 1.31 [1.08-1.58] and 1.15 [1.01-1.31] for 3 d and 7 d, respectively). We also observed no association between IDTs and IS, or the risk ratio was close to unity. IDTs did not appear to be associated with a transient risk of MI and IS in the Taiwanese population, with consistent findings from both case-only study designs. However, we cannot exclude that dental infections and diseases may yield a long-term risk of MI and IS.

Genetic profiles of transcriptomic clusters of childhood asthma determine specific severe subtype.

BACKGROUND: Previous studies have defined transcriptomic subtypes of adult asthma using samples of induced sputum and bronchial epithelium; however, those procedures are not readily applicable in the clinic, especially for childhood asthma. OBJECTIVE: We aim to dissect the transcriptomic clusters of childhood asthma using highly variably expressed genes of peripheral blood mononuclear cells (PBMC) among patients. METHODS: Gene expression of PBMC from 133 asthmatic children and 11 healthy controls was measured with Illumina microarrays. We applied the k-means clustering algorithm of 2048 genes to assign asthmatic children into clusters. Genes with differential expression between asthma clusters and healthy controls were used to investigate whether they could identify severe asthma of children and adults. RESULTS: We identified 3 asthma clusters with distinct inflammatory profiles in peripheral blood. Cluster 1 had the highest eosinophil count. Cluster 2 showed lower counts of both eosinophils and neutrophils. Cluster 3 had the highest neutrophil count and the poorest treatment control. Compared with other patients, Cluster 3 exhibited a unique gene expression pattern which was associated with changes in the glucocorticoid signalling and activation of the T helper 1/T helper 17 (TH 1/TH 17) immune pathways. In the validation studies, an 84-gene signature could identify severe asthma in children on leucocytes, as well as severe asthma in adults on CD8+ T cells. CONCLUSIONS AND CLINICAL RELEVANCE: Gene expression profiling of PBMC is useful for the identification of TH 1/TH 17-mediated asthma with poor treatment control. PBMC and CD8+ T cells could be important targets for the investigation and identification of severe asthma.

Periodontitis and dental scaling associated with pyogenic liver abscess: A population-based case-control study.

BACKGROUND AND OBJECTIVES: The purpose of this study was to investigate the relationship between periodontitis, dental scaling (DS) and pyogenic liver abscesses (PLAs). MATERIAL AND METHODS: A nationwide population-based case-control study was applied using data from the National Health Insurance Research Database in Taiwan. We identified and enrolled 691 PLA patients, who were individually matched by age and sex to 2764 controls. RESULTS: Conditional logistic regression was applied to estimate adjusted odds ratios (aORs) in patients with exposure to periodontitis and DS before PLA. After adjusting for other confounding factors, periodontitis remained a risk factor for PLA among patients aged 20-40 years, with an aOR of 2.31 (95% confidence interval [CI] = 1.37-3.90, P = .0018). In addition, the average aOR for PLA was significantly lower among patients with one DS (aOR = 0.76, 95% CI = 0.59-0.96) and more than one DS (aOR = 0.61, 95% CI = 0.39-0.95) within 1 year before the index date. CONCLUSION: According to these results, we concluded that adult patients with periodontitis aged <50 years old are more at risk for PLA than controls, particularly when they have no DS. Moreover, from 20 years of age, non-periodontal patients subjected to at least 2 DS per year are less at risk for PLA than controls.

Childhood asthma clusters reveal neutrophil-predominant phenotype with distinct gene expression.

BACKGROUND: Childhood asthma comprises different phenotypes with complex pathophysiology. Different asthma phenotypes evoke various clinical symptoms and vary in their responses to treatments. METHODS: We applied k-means clustering algorithm of twelve objective laboratory tests among 351 asthmatic children enrolled in the Taiwanese Consortium of Childhood Asthma Study (TCCAS). We constructed gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with different asthma phenotypes. RESULTS: Five distinct phenotypes of childhood asthma were identified and can be characterized by either eosinophil-predominant or neutrophil-predominant inflammatory characteristics. In the gene expression profile analysis, significant differences were noted for neutrophil-predominant asthma, compared with samples from all the other asthma phenotypes. The vast majority of the differentially expressed genes in neutrophil-predominant asthma was associated with corticosteroid response. From an independent inhaled corticosteroid (ICS) response cohort, we also found neutrophils could be activated in this severe asthma phenotype and neutrophil-predominant asthma may be associated with corticosteroid nonresponsiveness. CONCLUSION: Phenotype clustering of childhood asthma can be helpful to identify clinically relevant patients and reveal different inflammatory characteristics in asthmatic children. Neutrophil-predominant asthma is the most severe asthma phenotype with poor corticosteroid response. Gene expression profile of different asthma phenotypes not only improve our knowledge of childhood asthma, but also can guide asthma precision medicine.

Effect of ultraviolet light, organic acids, and bacteriophage on Salmonella populations in ground beef.

This study investigated individual and combined effects of organic acids, bacteriophages, and ultraviolet light interventions on Salmonella populations in ground beef. Beef trim was inoculated with four Salmonella strains to result in a contamination level of 3.5 log CFU/g after grinding. Lactic (LA) and peroxyacetic (PAA) acids, bacteriophages (S16 and FO1a) (BA), and ultraviolet light (UV) were applied on fresh trim prior to grinding. Applications of individual or combined organic acids did not significantly decrease Salmonella populations in ground beef. Individual applications of BA and UV light decreased approximately 1 log CFU/g (P<0.05). Combined applications of BA and UV provided an optimal decrease of 2 log CFU/g (P<0.05). Organic acid applications do not reduce Salmonella populations in ground beef when applied on trim prior to grinding. Combined applications of UV and BA may be used in industry settings to improve Salmonella control in ground beef.

Evaluation of palatability and muscle composition of novel value-added beef cuts.

The aim of this study was to evaluate the muscle profile of novel added-value beef cuts including the caudal tip of the M. infraspinatus (Bonanza Cut; TIP) and M. subscapularis (SUB) and two traditional sirloin steak cuts, M. gluteus medius (top sirloin; GLM) and M. rectus femoris (sirloin tip; REC). Samples were subjected to Warner-Braztler Shear Force (WBSF), sensory, cooking loss, and proximate analysis. The muscle TIP had superior values of subjective tenderness, juiciness, and slight off-flavor intensity when compared to all other muscles. The TIP and SUB were similar in WBSF. Cooking loss and moisture values of raw samples were lowest for TIP. Results suggest that TIP can provide enhanced eating experience for consumers and improved marketability for the meat industry.

Association between thyroid dysfunction and dysglycaemia: a prospective cohort study.

AIMS: To compare the incidence of hyperglycaemia among participants with low, elevated and normal serum thyroid-stimulating hormone concentration, as well as the incidence of abnormal thyroid function test results among participants with normal blood glucose and those with hyperglycaemia. METHODS: In a prospective study, a cohort of 72 003 participants with normal, low and elevated serum thyroid-stimulating hormone concentration were followed from the study beginning to the first report of diabetes and prediabetes. A proportional hazards regression model was used to calculate the hazard ratios and 95% CIs for each outcome, adjusting for age, sex, education level, smoking, alcohol consumption and obesity. Analyses for the association between dysglycaemia and incident abnormal thyroid function test were also conducted. RESULTS: During a median 2.6 year follow-up, the incident rates for dysglycaemia, particularly prediabetes, were substantially higher in participants with elevated thyroid-stimulating hormone concentrations at baseline, while the rates for participants with normal and low thyroid-stimulating hormone were similar. After controlling for risk factors, participants with elevated thyroid-stimulating hormone retained a 15% increase in risk of prediabetes (adjusted hazard ratio 1.15, 95% CI 1.04-1.26), but were not at greater risk of diabetes (adjusted hazard ratio 0.96, 95% CI 0.64-1.44). By contrast, participants with normal and low thyroid-stimulating hormone concentrations had similar dysglycaemia risks. Participants with diabetes and prediabetes were not at greater risks of developing abnormal thyroid function test results when compared with participants with euglycaemia. CONCLUSIONS: People with elevated serum thyroid-stimulating hormone concentration are at greater risk of developing prediabetes. Whether this includes a greater risk of developing frank diabetes may require an extended period of follow-up to clarify.

Effects of long spray-chilling on water pocket development in ribeyes.

Water Pocket (WP) is a defect on beef that may lead to significant economic losses. Our hypothesis is that longer spray-chilling time increases WP incidence on ribeyes (M. longissimus thoracis). Ribeyes (28,801) were visually evaluated for the presence of WP after 24 or 72h of spray chilling. Additionally, 252 beef sides were evaluated prior to chilling to predict WP development after 24h of spray chilling. Also, the 12th rib fat thickness was measured on 313 sides and the sides were assigned to two categories of WP or no WP to evaluate fat thickness as an indicator for WP. Subcutaneous fat softness is not related to WP development, longer spray-chilling does not increase the incidence of WP in ribeyes, and thinner subcutaneous fat is an indicator for WP development.

Bacteriophage application on red meats and poultry: Effects on Salmonella population in final ground products.

This research was conducted to study the effects of bacteriophage application during tumbling on Salmonella populations in ground meat and poultry. Red meat trim and poultry were inoculated with a Salmonella cocktail to result in a contamination level of 7logCFU/g in ground products. A commercial preparation containing bacteriophages S16 and Felix-O1a (FO1a) was applied during tumbling at 107 and 108PFU/ml. Samples were held at 4°C for 6h and 18h (red meat) and 30min and 6h (poultry). Overall, bacteriophage application on trim reduced 1 and 0.8logCFU/g of Salmonella in ground beef and ground pork, respectively. For ground chicken and ground turkey, Salmonella was reduced by 1.1 and 0.9logCFU/g, respectively. This study shows that bacteriophage application during tumbling of red meat trim and poultry can provide additional Salmonella control in ground products.