Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Her3 in gastric cancer and its association with molecular prognostic markers: a Saudi cohort based study

ABSTRACT Her 3 is a member of epidermal growth factor receptors. Mutated, oncogenic Her3 is reported in gastric and colonic cancers with emerging evidence that Her3 can be a potential target for molecular therapies. There is a paucity of studies regarding Her3 and its prognostic implications in gastric cancer in our region. In this study, we evaluated prevalence of Her3 in gastric cancer, in a Saudi cohort of cases, along with its association with prognostic markers p53 and Ki-67. The study was conducted in Department of Pathology of King Fahd Hospital of Imam Abdulrahman Bin Faisal University, Dammam, KSA. Fifty cases of gastric carcinoma were selected from the pathology files that fulfilled the inclusion criteria. Clinico-pathological parameters, Laurens histological classification, and immunohistochemical staining for Her3, p53, and Ki-67 were done. Her 3 positive cases were also evaluated for Her-2neu co-expression. Her3 positivity was seen in 16% (n = 8) out of a total of 50 cases. The median age of presentation was 44 years. Within Her3 positive cases, a female preponderance of 63% (n = 5), presence of high grade tumors in 75% (n = 6), diffuse gastric carcinoma in 63% (n = 5), diffuse to focal p53 positivity in 63% (n = 5), and a high to moderate Ki-67 proliferation index in 75% (n = 6) of cases was seen. Her3 expression was independent of Her-2neu status. Her3 prevalence of 16% with a median age of 44 years at presentation was less than in other reported studies, highlighting the concept of ethnic and regional variation in tumor characteristics. Her3 association with diffuse gastric carcinoma, high grade tumors, diffuse to focal p53 positivity and high to moderate Ki-67 proliferation index points towards a more aggressive clinical behavior.
MicroRNA-338-3p inhibits the progression of bladder cancer through regulating ETS1 expression.

OBJECTIVE MicroRNA-338-3p (miR-338-3p) was reported to influence the metastasis and development of several human cancers. However, in bladder cancer (BC), the special function of miR-338-3p remains unknown. Here, we aimed at exploring the miR-338-3p function in the progression of BC. PATIENTS AND METHODS miR-338-3p and ETS1 expressions were examined by quantitative Real-time polymerase chain reaction (qRT-PCR) in BC samples. Following that, transwell assays for cell migration and invasion were performed. And MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay for cell proliferation was conducted as well. Western blot was employed to examine the epithelial-mesenchymal transition (EMT) marker expressions. Finally, the relationship between miR-338-3p and E26 transformation specific-1 (ETS1) was verified by luciferase reporter assay. RESULTS The decreased miR-338-3p expression was examined in BC cells. Moreover, miR-338-3p upregulation repressed cell proliferation ability in BC. Next, miR-338-3p upregulation also depressed cell metastasis and EMT in BC cells. Furthermore, ETS1 was a direct target of miR-338-3p and inversely associated with its expression. And upregulation of ETS1 partially rescued the suppression of miR-338-3p for cell proliferation and metastasis in BC. CONCLUSIONS Upregulation of miR-338-3p inhibited the proliferation, metastasis and EMT in BC by suppressing ETS, showing that miR-338-3p might block the development of BC through regulating ETS1 expression.
Functional Development of Principal Neurons in the Anteroventral Cochlear Nucleus Extends Beyond Hearing Onset

Sound information is transduced into graded receptor potential by cochlear hair cells and encoded as discrete action potentials of auditory nerve fibers. In the cochlear nucleus, auditory nerve fibers convey this information through morphologically distinct synaptic terminals onto bushy cells (BCs) and stellate cells (SCs) for processing of different sound features. With expanding use of transgenic mouse models, it is increasingly important to understand the in vivo functional development of these neurons in mice. We characterized the maturation of spontaneous and acoustically evoked activity in BCs and SCs by acquiring single-unit juxtacellular recordings between hearing onset (P12) and young adulthood (P30) of anesthetized CBA/J mice. In both cell types, hearing sensitivity and characteristic frequency (CF) range are mostly adult-like by P14, consistent with rapid maturation of the auditory periphery. In BCs, however, some physiological features like maximal firing rate, dynamic range, temporal response properties, recovery from post-stimulus depression, first spike latency (FSL) and encoding of sinusoid amplitude modulation undergo further maturation up to P18. In SCs, the development of excitatory responses is even more prolonged, indicated by a gradual increase in spontaneous and maximum firing rates up to P30. In the same cell type, broadly tuned acoustically evoked inhibition is immediately effective at hearing onset, covering the low- and high-frequency flanks of the excitatory response area. Together, these data suggest that maturation of auditory processing in the parallel ascending BC and SC streams engages distinct mechanisms at the first central synapses that may differently depend on the early auditory experience.
Reversal of direct oral anticoagulants: Guidance from the Anticoagulation Forum

Two specific reversal agents for direct oral anticoagulants (DOACs) have been approved in the United States: idarucizumab for dabigatran reversal and andexanet alfa for apixaban and rivaroxaban reversal. Non‐specific prohemostatic agents such as prothrombin complex concentrate (PCC) and activated PCC have also been used for DOAC reversal. The goal of this document is to provide comprehensive guidance from the Anticoagulation Forum, a North American organization of anticoagulation providers, regarding use of DOAC reversal agents. We discuss indications for reversal, provide guidance on how the individual reversal agents should be administered, and offer suggestions for stewardship at the health system level.
Effects of Childhood-onset Inflammatory Bowel Disease on School Performance: A Nationwide Population-based Cohort Study Using Swedish Health and Educational Registers.

BACKGROUND Childhood-onset inflammatory bowel disease (IBD) might negatively impact academic school performance. We conducted a nationwide study to examine the association between childhood-onset IBD and school results. METHODS Our study population was selected from Swedish health registers. In the National Patient Register (1990 to 2013), we identified 2827 children with IBD: Crohn's disease (CD), n = 1207, and ulcerative colitis (UC), n = 1370. Patients were matched with 10 reference individuals by age, sex, birth year, and place of residence (n = 28,235). Final compulsory school grades (0 to 320 grade points) and qualification for high school (yes or no) were obtained through the National School Register. Regression models controlling for socioeconomic factors were used to analyze the association of IBD with school performance. RESULTS Children with IBD had a lower final grade point average (adjusted mean grade difference [AMGD] -4.9, 95% confidence interval [CI] -7.1 to -2.6) but not a significantly higher risk to not qualify for high school (odds ratio [OR] 1.14, CI 0.99-1.31). The results were similar in children with UC (AMGD -5.5, CI -8.7 to -2.3) and CD (AMGD -4.7, CI -8.2 to -1.2). Underperformance was more common in subsets of IBD children characterized by markers associated with long-standing active disease (eg, >30 inpatient days [AMGD-18.1, CI -25.8 to -10.4]). CONCLUSION Most children with IBD achieve comparable results in the final year of compulsory school as their healthy peers. Care should be improved for the subgroup of children for which IBD has a stronger negative impact on school performance.
Peritoneal Ultrafiltration in the Long-Term Treatment of Chronic Heart Failure Refractory to Pharmacological Therapy

Introduction Despite continuous improvement in the treatment, heart failure (HF) is a growing health problem and a major cause of mortality and morbidity in the world. There is some positive experience with the removal of the fluid excess via peritoneum in those patients, regardless of their renal function. The aim of this single center pilot study was to assess the efficacy of peritoneal ultra filtration (PUF) with a nightly 12-h exchange in the long-term treatment of refractory HF. Methods The study included patients with chronic HF resistant to updated HF therapy (pharmacological and devices if applicable), who had experienced at least three hospitalizations due to HF during the preceding year and were disqualified from heart transplantation. All of them were treated with nightly 12-h 7.5% icodextrin exchange. Results There were 15 patients (13 men), aged 72 ± 9 years, with charlson comorbidity index (CCI) 9 ± 1.2, NYHA class IV (11 patients) or III (4 patients), and eGFR 32 ± 11 ml/min/1.73m2. They were followed up for 24 ± 8 months (range 12–43, median 26 months). During the 1st year, all patients improved their NYHA functional class from 3.7 ± 0.5 to 2.6 ± 0.5; P = 0.0005, with stable (34.3 ± 12.4, and 35.6 ± 16.5%, respectively) left ventricular ejection fraction (LVEF), and inferior vena cava (IVC) diameter decreased from 27.8 ± 2.7 to 24.4 ± 3.4 mm; P = 0.09. Daily diuresis increased from 867 ± 413 to 1221 ± 680 ml; P = 0.25, while the dose of furosemide could be reduced from 620 ± 256 to 360 ± 110 mg/d; P = 0.0005, however, the kidney function deteriorated, with eGFR drop from 32 ± 11 to 25.6 ± 13 ml/min/1.73m2; P = 0.01). HF-related hospitalizations decreased from 8.9 ± 2.8 days/month to 1.5 ± 1.2 days/month (P = 0.003). Mechanical peritoneal dialysis complications occurred in five patients and infectious complications in four (peritonitis rate 1 per 72 patient-month). Patient survival was 93% at 1 year and 73% at 2 year. Technique survival was 100%. Conclusion In patients with refractory HF, PUF with one overnight icodextrin exchange appears to be a promising therapeutic option as an adjunct to pharmacological management of those who are not transplant candidates. It should be emphasized that the treatment can have a great impact on the quality of life and the total costs of treating these patients.
Synergistic potential of Juniperus communis and Helichrysum italicum essential oils against nontuberculous mycobacteria.

OBJECTIVE The present study evaluated the possible synergistic antimycobacterial interactions of Juniperus communis and Helichrysum italicum essential oils (EO). METHODS Antimycobacterial potential was tested against Mycobacterium avium and Mycobacterium intracellulare using broth and water dilution method and checkerboard synergy method. Antiadhesion and antibiofilm effect of EOs was evaluated on biotic (HeLa cells) and abiotic surface (polystyrene). To evaluate the possible mechanisms of action, cellular leakage of proteins and DNA was tested and structural changes were visualized with a transmission electron microscope. RESULTS MIC, minimum bactericidal concentration (MBC) and minimal effective concentration (MEC) were 1.6 mg ml-1 for J. communis EO and 3.2 mg ml-1 for H. italicum EO against both mycobacteria. All combinations of EOs in checkerboard synergy method produced fractional inhibitory concentration index values ranging from 0.501 to 1.5, corresponding to synergistic, additive or indifferent effects. Mycobacterium avium showed a greater tendency to create biofilm but these EOs at subinhibitory concentrations (sMIC) effectively blocked the adhesion and the establishment of biofilm. The exposure of both mycobacteria to MICs and sMICs lead to significant morphological changes: acquired a swollen form, ghost-like cell, disorganized cytoplasm detached from the cell wall. OD value of supernatant for both mycobacteria exposed to EOs have confirmed that there is a leakage of cellular material. CONCLUSION The leakage of the cellular material is noticeably higher in sMIC, which is probably due to cell wall damage. sMIC of both EOs have an additive or synergistic effect, reducing MICs, limiting adhesion and preventing the formation of biofilms.
Bacterial content and associated risk factors influencing the quality of bulk tank milk collected from dairy cattle farms in Mandalay Region

Abstract To investigate the bacterial content and risk factors associated with the hygienic quality of raw milk, a cross‐sectional study was conducted in four townships of Mandalay Region, Myanmar. From April to October 2017, bulk tank milk samples (n = 233) were collected from 233 dairy cattle farms located in Tada‐U, Pyin Oo Lwin, Meiktila, and Patheingyi Townships. From each farm, approximately 100 ml of bulk tank milk was collected and examined for bacterial content. Total bacterial count (TBC) and coliform count (CC) in milk samples were determined using milk agar and violet red bile agar. Of 233 milk samples, 68.2% (159/233) showed TBC higher than 1.0 × 105 cfu/ml, and 78.4% (183/233) showed CC higher than 100 cfu/ml. The mean value of TBC among 233 farms was 2.55 × 107 cfu/ml, ranging from 6.0 × 103 to 3.0 × 109 cfu/ml, whereas the mean value of CC was 1.59 × 105 cfu/ml, ranging from 10 to 8.4 × 106 cfu/ml. TBC tended to increase as CC increased in milk samples. The number of precautionary measures for milking operation, choice of cleaning materials, training experience of the farmers, cleanliness score of milking cows, and CMT scores of milk were significantly associated (p < 0.05) with TBC in bulk tank milk. Similarly, the number of precautionary measures for milking operation, choice of cleaning materials, training experience of the farmers, cleanliness scores of milking cows, CMT scores of milk samples, herd size, and type of milking practice showed significant association (p < 0.05) with CC in bulk tank milk. The effects of these potential risk factors should be minimized, farmers should be trained properly, and technical support should be provided, so that the quality of raw milk produced in Myanmar can be improved.
Measuring price discovery between nearby and deferred contracts in storable and nonstorable commodity futures markets

Futures market contracts with varying maturities are traded concurrently and the speed at which they process information is of value in understanding the pricing discovery process. Using price discovery measures, including Putnins (2013) information leadership share and intraday data, we quantify the proportional contribution of price discovery between nearby and deferred contracts in the corn and live cattle futures markets. Price discovery is more systematic in the corn than in the live cattle market. On average, nearby contracts lead all deferred contracts in price discovery in the corn market, but have a relatively less dominant role in the live cattle market. In both markets, the nearby contract loses dominance when its relative volume share dips below 50%, which occurs about 2-3 weeks before expiration in corn and 5-6 weeks before expiration in live cattle. Regression results indicate that the share of price discovery is most closely linked to trading volume but is also affected, to far less degree, by time to expiration, backwardation, USDA announcements and market crashes. The effects of these other factors vary between the markets which likely reflect the difference in storability as well as other market-related characteristics.
Shelf life study of Bolu Cukke using the Accelerated Shelf Life Testing (ASLT) method

The aim of this study was to determine the shelf life of Bolu Cukke in glazed paper packaging using the Accelerated Shelf Life Testing (ASLT) Method. Determination of shelf life using the ASLT method by knowing the critical moisture content and equilibrium content in Bolu Cukke. The results of critical moisture content and equilibrium content of Bolu Cukke indicate a number 2 indicating that it is at a critical point, shelf life is 6 days, with critical water content as much as 23.49% while the results using a 7-day labuza calculation showed no significant difference by storing it using critical water content. The results of the equilibrium value of 24.606% by producing a slope b value of 0.307 using the Henderson isothermic absorption curve with an MRD value of 3.1915. Estimation of shelf life of Bolu Cukke products using the labuza equation shows that the shelf life for Bolu Cukke products is 7 using glasin paper packaging which to protect the product from sunlight, air, and contamination of microorganisms. The change affected physically, chemically and microbiologically, which makes bolu cukke can no longer be consumed.
A high baryon fraction in massive haloes at z ∼ 3

We investigate the baryon content of the circumgalactic medium (CGM) within the virial radius of $M_h \sim 10^{12} \; M_\odot$ haloes at z ~ 3, by modelling the surface brightness profile of the giant Ly$\alpha$ nebulae recently discovered by MUSE around bright QSOs at this redshift. We initially assume fluorescent emission from cold photo-ionized gas confined by the pressure of a hot halo. Acceptable CGM baryon fractions (equal or smaller than the cosmological value) require that the cold gas occupies $\lesssim$ 1% of the volume, but is about as massive as the hot gas. CGM baryon fractions as low as 30% of the cosmic value, as predicted by some strongly ejective feedback models at this redshift, are not easy to reconcile with observations, under our assumptions, unless both the QSO-hosting haloes at $z\sim3$ are more massive than recent BOSS estimates based on clustering and the photo-ionized gas is colder than expected in a standard QSO ionizing radiation field. We also consider the option that the emission is dominated by photons scattered from the QSO broad line region. In this scenario, a very stringent lower limit to the baryon fraction can be obtained under the extreme assumption of optically thin scattering. We infer in this case a baryon fraction of at least 70% of the cosmic value, for fiducial parameters. Lower values require halo masses or gas temperatures different than expected, or that some mechanism keeps the cold gas systematically over-pressured with respect to the ambient medium.
Aggregating Google Trends: Multivariate Testing and Analysis

Web search data are a valuable source of business and economic information. Previous studies have utilized Google Trends web search data for economic forecasting. We expand this work by providing algorithms to combine and aggregate search volume data, so that the resulting data is both consistent over time and consistent between data series. We give a brand equity example, where Google Trends is used to analyze shopping data for 100 top ranked brands and these data are used to nowcast economic variables. We describe the importance of out of sample prediction and show how principal component analysis (PCA) can be used to improve the signal to noise ratio and prevent overfitting in nowcasting models. We give a finance example, where exploratory data analysis and classification is used to analyze the relationship between Google Trends searches and stock prices.
Multiple Treatments with Strategic Interaction

We develop an empirical framework to identify and estimate the effects of treatments on outcomes of interest when the treatments are the result of strategic interaction (e.g., bargaining, oligopolistic entry, peer effects). We consider a model where agents play a discrete game with complete information whose equilibrium actions (i.e., binary treatments) determine a post-game outcome in a nonseparable model with endogeneity. Due to the simultaneity in the first stage, the model as a whole is incomplete and the selection process fails to exhibit the conventional monotonicity. Without imposing parametric restrictions or large support assumptions, this poses challenges in recovering treatment parameters. To address these challenges, we first establish a monotonic pattern of the equilibria in the first-stage game in terms of the number of treatments selected. Based on this finding, we derive bounds on the average treatment effects (ATEs) under nonparametric shape restrictions and the existence of excluded exogenous variables. We show that instrument variation that compensates strategic substitution helps solve the multiple equilibria problem. We apply our method to data on airlines and air pollution in cities in the U.S. We find that (i) the causal effect of each airline on pollution is positive, and (ii) the effect is increasing in the number of firms but at a decreasing rate.
FakeNewsNet: A Data Repository with News Content, Social Context, and Spatiotemporal Information for Studying Fake News on Social Media

Social media has become a popular means for people to consume and share the news. At the same time, however, it has also enabled the wide dissemination of fake news, that is, news with intentionally false information, causing significant negative effects on society. To mitigate this problem, the research of fake news detection has recently received a lot of attention. Despite several existing computational solutions on the detection of fake news, the lack of comprehensive and community-driven fake news data sets has become one of major roadblocks. Not only existing data sets are scarce, they do not contain a myriad of features often required in the study such as news content, social context, and spatiotemporal information. Therefore, in this article, to facilitate fake news-related research, we present a fake news data repository FakeNewsNet, which contains two comprehensive data sets with diverse features in news content, social context, and spatiotemporal information. We present a comprehensive description of the FakeNewsNet, demonstrate an exploratory analysis of two data sets from different perspectives, and discuss the benefits of the FakeNewsNet for potential applications on fake news study on social media.
Tests for Forecast Instability and Forecast Failure under a Continuous Record Asymptotic Framework

We develop a novel continuous-time asymptotic framework for inference on whether the predictive ability of a given forecast model remains stable over time. We formally define forecast instability from the economic forecaster's perspective and highlight that the time duration of the instability bears no relationship with stable period. Our approach is applicable in forecasting environment involving low-frequency as well as high-frequency macroeconomic and financial variables. As the sampling interval between observations shrinks to zero the sequence of forecast losses is approximated by a continuous-time stochastic process (i.e., an Ito semimartingale) possessing certain pathwise properties. We build an hypotheses testing problem based on the local properties of the continuous-time limit counterpart of the sequence of losses. The null distribution follows an extreme value distribution. While controlling the statistical size well, our class of test statistics feature uniform power over the location of the forecast failure in the sample. The test statistics are designed to have power against general form of insatiability and are robust to common forms of non-stationarity such as heteroskedasticty and serial correlation. The gains in power are substantial relative to extant methods, especially when the instability is short-lasting and when occurs toward the tail of the sample.