Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombinant human amelogenin reverses osteogenesis suppression induced by an inflammatory microenvironment in human periodontal ligament cells

Objective: The purpose of our study was to investigate the effects of recombinant human amelogenin (rHAm) on the osteogenic differentiation of PDLCs and to examine the role of Wnt/β-catenin signaling in PDLCs in the inflammatory microenvironment in vitro. Study Design: The proliferation rate of PDLCs was tested by MTT assay. The osteogenic differentiation of PDLCs under treatment with P. gingivalis LPS or rHAm was examined by real-time PCR and Western blotting. The gene and protein expression of Wnt signaling molecules was detected by real-time PCR and Western blotting, respectively. Data were analyzed statistically using the SPSS13.0 software package. Results: Our results show that 20 μg/mL rHAm can promote the proliferation of PDLCs, and 10 μg/mL P. gingivalis LPS has an inhibitory effect on these cells. The expression of osteogenic factors is significantly decreased in the 10 μg/mL P. gingivalis LPS group but is increased in the 20 μg/mL rHAm group. ALP activity also can be improved by rHAm under an inflammatory microenvironment. After treatment with P. gingivalis LPS, the mRNA expression of Wnt1, LRP5/6 and β-catenin in PDLCs decreases. Conclusion: Our data indicate that rHAm could improve the activity of osteogenic differentiation under an inflammatory microenvironment.
Perioperative and Survival Outcomes Following Neoadjuvant FOLFIRINOX versus Gemcitabine Abraxane in Patients with Pancreatic Adenocarcinoma.

Context Neoadjuvant chemotherapy is increasingly used in borderline resectable and locally advanced pancreatic cancer to facilitate surgical resection. Objective To compare progression free survival and overall survival in patients receiving neoadjuvant FOLFIRINOX with those receiving gemcitabine/abraxane. Design Retrospective cohort study. Setting University of Colorado Hospital from 2012-2016. Participants Patients with pancreatic adenocarcinoma. Interventions Neoadjuvant FOLFIRINOX or gemcitabine/abraxane. Outcome Measures Perioperative outcomes, progression free survival, and overall survival were compared between groups. A multivariate Cox proportional hazard model was applied to evaluate survival outcomes. Results We identified 120 patients: 83 (69.2%) FOLFIRINOX and 37 (30.8%) gemcitabine/abraxane. The FOLIFRINOX group was younger and had a lower ECOG performance status (p<0.05). Patients in the FOLFIRINOX group were more likely to undergo surgical resection compared to gemcitabine/abraxane (66.3% vs. 32.4%, p=0.002). Among all patients, median follow up was 16.9 months and FOLFIRINOX was associated with improved PFS (15.3 vs. 8.2 months, p=0.006), but not overall survival (23.5 vs. 18.7 months, p=0.228). In these patients, insulin-dependent diabetes was associated with a worse progression free survival and overall survival and surgical resection was protective. Among surgically resected patients, median follow up was 21.1 months and there was no difference in progression free survival (19.5 vs. 15.1 months) or overall survival (27.4 vs. 19.8 months) between the FOLFIRINOX and gemcitabine/abraxane groups, respectively (p>0.05). Insulin-dependent diabetes and a poor-to-moderate pathologic response was associated with worse progression free survival and overall survival. Conclusion Neoadjuvant FOLFIRINOX may improve progression free survival by increasing the proportion of patients undergoing surgical resection. Improved understanding of the role for selection bias and longer follow up are needed to better define the impact of neoadjuvant FOLFIRINOX on overall survival.
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis

Motivation Parameter estimation methods for ordinary differential equation (ODE) models of biological processes can exploit gradients and Hessians of objective functions to achieve convergence and computational efficiency. However, the computational complexity of established methods to evaluate the Hessian scales linearly with the number of state variables and quadratically with the number of parameters. This limits their application to low‐dimensional problems. Results We introduce second order adjoint sensitivity analysis for the computation of Hessians and a hybrid optimization‐integration‐based approach for profile likelihood computation. Second order adjoint sensitivity analysis scales linearly with the number of parameters and state variables. The Hessians are effectively exploited by the proposed profile likelihood computation approach. We evaluate our approaches on published biological models with real measurement data. Our study reveals an improved computational efficiency and robustness of optimization compared to established approaches, when using Hessians computed with adjoint sensitivity analysis. The hybrid computation method was more than 2‐fold faster than the best competitor. Thus, the proposed methods and implemented algorithms allow for the improvement of parameter estimation for medium and large scale ODE models. Availability and implementation The algorithms for second order adjoint sensitivity analysis are implemented in the Advanced MATLAB Interface to CVODES and IDAS (AMICI, https://github.com/ICB‐DCM/AMICI/). The algorithm for hybrid profile likelihood computation is implemented in the parameter estimation toolbox (PESTO, https://github.com/ICB‐DCM/PESTO/). Both toolboxes are freely available under the BSD license.
Role of supplemental oxygen in reducing surgical site infection in acute appendicities: Our experience of sixty four cases

Aim : To assess whether use of 80% oxygen reduces the frequency of surgical site infection in patients undergoing open appendectomy for appendicitis. Material & Methods : A randomised control study was conducted in the department of general surgery at NKP Salve Institute of Medical Sciences & Research Center & Lata Mangeshkar Hospital Nagpur. Sixty four patients undergoing open appendectomy via incision in the right lower quadrant of the abdomen were divided randomly into study group ie. patients receiving 80% oxygen during anesthesia, followed by high-flow oxygen for 2 hours in the recovery room and the control group receiving 30% oxygen, as usual. Surgical site infection will be assessed by the ASEPSIS (additional treatment, serous discharge, erythema, purulent discharge, separation of deep tissues, isolation of bacteria, and stay in hospital prolonged >14 days) system score. SPSS statistical software version 16.0 was used for data analysis. Results : The age distribution between the study and control group was statistically similar with p = 0.627. The sex distribution between the study and control group was statistically similar with p = 0.157. There were no medical comorbidities seen in both groups. The body temperature distribution between the study [mean SD = 37.020. 12)] and control [mean SD = 37.06(0.24))] group was statistically similar with p = 0.272. Duration of abdominal pain was not significant with p=0.596. Preoperative analysis like WBC count, abdominal tenderness, Abdominal rigidity, hemoglobin, serum creatinine, blood urea, USG abdomen distribution was statistically not significant with p value >0.05. Duration of operation distribution between the groups was not significant with p=0.874. There was no surgical site infection seen in study as well as control group. All the cases in study as well as control group have satisfactory healing. There was significant (p=0.003) longer hospital stay in control group. Conclusion : Our study concludes that there is no role of supplemental oxygen in reducing surgical site infection in acute appendicitis.
Anti-Insulin B Cells Are Poised for Antigen Presentation in Type 1 Diabetes

Early breaches in B cell tolerance are central to type 1 diabetes progression in mouse and man. Conventional BCR transgenic mouse models (VH125.Tg NOD) reveal the power of B cell specificity to drive disease as APCs. However, in conventional fixed IgM models, comprehensive assessment of B cell development is limited. To provide more accurate insight into the developmental and functional fates of anti-insulin B cells, we generated a new NOD model (VH125SD.NOD) in which anti-insulin VDJH125 is targeted to the IgH chain locus to generate a small (1–2%) population of class switch–competent insulin-binding B cells. Tracking of this rare population in a polyclonal repertoire reveals that anti-insulin B cells are preferentially skewed into marginal zone and late transitional subsets known to have increased sensitivity to proinflammatory signals. Additionally, IL-10 production, characteristic of regulatory B cell subsets, is increased. In contrast to conventional models, class switch–competent anti-insulin B cells proliferate normally in response to mitogenic stimuli but remain functionally silent for insulin autoantibody production. Diabetes development is accelerated, which demonstrates the power of anti-insulin B cells to exacerbate disease without differentiation into Ab-forming or plasma cells. Autoreactive T cell responses in VH125SD.NOD mice are not restricted to insulin autoantigens, as evidenced by increased IFN-γ production to a broad array of diabetes-associated epitopes. Together, these results independently validate the pathogenic role of anti-insulin B cells in type 1 diabetes, underscore their diverse developmental fates, and demonstrate the pathologic potential of coupling a critical β cell specificity to predominantly proinflammatory Ag-presenting B cell subsets.
Smart Wound Dressings for Diabetic Chronic Wounds

Given their severity and non-healing nature, diabetic chronic wounds are a significant concern to the 30.3 million Americans diagnosed with diabetes mellitus (2015). Peripheral arterial diseases, neuropathy, and infection contribute to the development of these wounds, which lead to an increased incidence of lower extremity amputations. Early recognition, debridement, offloading, and controlling infection are imperative for timely treatment. However, wound characterization and treatment are highly subjective and based largely on the experience of the treating clinician. Many wound dressings have been designed to address particular clinical presentations, but a prescriptive method is lacking for identifying the particular state of chronic, non-healing wounds. The authors suggest that recent developments in wound dressings and biosensing may allow for the quantitative, real-time representation of the wound environment, including exudate levels, pathogen concentrations, and tissue regeneration. Development of such sensing capability could enable more strategic, personalized care at the onset of ulceration and limit the infection leading to amputation. This review presents an overview of the pathophysiology of diabetic chronic wounds, a brief summary of biomaterial wound dressing treatment options, and biosensor development for biomarker sensing in the wound environment.
Diffusion properties of active particles with directional reversal

The helical structure of DNA imposes constraints on the rate of diffusionlimited protein binding. Here we solve the reaction–diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general. S Online supplementary data available from stacks.iop. org/JPA/49/364002/ mmedia
The Mechanism of Peritoneal Fibrosis in Peritoneal Dialysis

Peritoneal fibrosis (PF) is a common morphological change in peritoneal dialysis (PD) patients. With the progression of PF, peritoneal membrane function is impaired, which leads to ultrafiltration failure. Furthermore, PF is an essential precursor condition for the development of encapsulating peritoneal sclerosis (EPS), which is the most serious complication of PD. Epithelial-mesenchymal transition (EMT) of peritoneal mesothelial cells (PMCs) plays a crucial role in PF. Transforming growth factor-? 1 (TGF-? 1) was thought to be the main regulator of EMT in PMCs. High glucose, hypertonicity, low pH, glucose degradation products and advanced glycation end-products in PD solution were suggested to induce TGF-? 1 production. In addition, chronic inflammation mediated by infiltration of immune cells and peritoneal angiogenesis also play pivotal roles for the progression of PF.
Cases in Psychiatry: A description of a multi-campus elective course for pharmacy students

Cases in Psychiatry was a multi-campus elective course aimed to expand psychiatry knowledge beyond the required course curriculum. The format of the class included didactic course work, small group discussion of patient cases and article evaluation, submission of written notes, debates, and script concordance test questions delivered via a live online platform. Based on student assessment and feedback at the end of the course, the elective course was determined to meet the prespecified course objectives.
Direction-of-arrival estimation of near-field sources based on compressed symmetric nested array and sparse signal reconstruction

In this paper, a novel underdetermined direction-of-arrival (DOA) estimation method based on compressed symmetric nested array and sparse signal representation is proposed in the near-field. Firstly, the forth order cumulants are employed to transform the original two-dimensional parameter estimation problem into a one-dimensional one and to obtain the difference co-array of the physical array. Then, in order to further increase the angular resolution and reduce the estimate error, the received signals of the virtual array are sparsely represented in spatial domain. Finally, the DOAs of the sources are founded through the use of the L1-regularized least square method. Compared to the existing methods, the proposed approach can process more sources and have lower variance and higher resolution. Simulation results are given to demonstrate the effectiveness and efficiency of the proposed method.
Inspiratory and expiratory resistance cause right‐to‐left bubble passage through the foramen ovale

A patent foramen ovale (PFO) is linked to increased risk of decompression illness in divers. One theory is that venous gas emboli crossing the PFO can be minimized by avoiding lifting, straining and Valsalva maneuvers. Alternatively, we hypothesized that mild increases in external inspiratory and expiratory resistance, similar to that provided by a SCUBA regulator, recruit the PFO. Nine healthy adults with a Valsalva‐proven PFO completed three randomized trials (inspiratory, expiratory, and combined external loading) with six levels of increasing external resistance (2–20 cmH2O/L/sec). An agitated saline contrast echocardiogram was performed at each level to determine foramen ovale patency. Contrary to our hypothesis, there was no relationship between the number of subjects recruiting their PFO and the level of external resistance. In fact, at least 50% of participants recruited their PFO during 14 of 18 trials and there was no difference between the combined inspiratory, expiratory, or combined external resistance trials (P > 0.05). We further examined the relationship between PFO recruitment and intrathoracic pressure, estimated from esophageal pressure. Esophageal pressure was not different between participants with and without a recruited PFO. Intrasubject variability was the most important predictor of PFO patency, suggesting that some individuals are more likely to recruit their PFO in the face of even mild external resistance. Right‐to‐left bubble passage through the PFO occurs in conditions that are physiologically relevant to divers. Transthoracic echocardiography with mild external breathing resistance may be a tool to identify divers that are at risk of PFO‐related decompression illness.
Simulation of Artificial Intelligence Agents using Modelica and the DLR Visualization Library

This paper introduces a scheme for testing artificial intelligence algorithms of autonomous systems using Modelica and the DLR Visualization Library. The simulation concept follows the ’Software-in-the-loop’ principle, whereas no adaptations are made to the tested algorithms. The environment is replaced by an artificial world and the rest of the autonomous system is modeled in Modelica. The scheme is introduced and explained by using the example of the ROboMObil, which is a robotic electric vehicle developed by the DLR’s Robotics and Mechatronics Center.
Food Sustainability in the Context of Human Behavior

The long-term goal of food sustainability is to produce enough food to maintain the human population. The intrinsic factors to guarantee a sustainable food system are a fertile land, water, fertilizers, a stable climate, and energy. However, as the world population grows, the volume of food needed in the future will not depend just on these intrinsic factors, but on human choices. This paper analyzes some of the human actions that may affect the sustainable future of the food supply chain, including diet, obesity, food miles, food waste, and genetically modified organisms.
Effect of nisin-producing Lactococcus lactis starter cultures on the inhibition of two pathogens in ripened cheeses

The effect of Lactococcus lactis nisin-producing strains, isolated from Italian fermented foods, onthe survival of two foodborne pathogens namely Listeria monocytogenes and Staphylococcus aureuswas investigated in experimental cheese production. One of the three Lactobacillus lactis nisin inn-oculated as starters, Lactobacillus lactis 41FL1 lowered S. aureus count by 1.73 log colony-formingunits (cfu)/g within the ﬁrst 3 days, reaching the highest reduction, 3.54 log cfu/g, by the end ofripening period of 60 days. There was no effect on L. monocytogenes. The application of L. lactis41FL1 as bioprotective culture in controlling S. aureus shows considerable promise.Keywords Lactococcus lactis, nisin, Staphylococcus aureus, Listeria monocytogenes, Cheese.INTRODUCTIONLactic acid bacteria (LAB) are widely used forthe fermentation and preservation of a widerange of milk, meat and vegetable foods.Among LAB strains, Lactococcus lactis isextensively used as starter culture in the dairyindustry, and the potential applications of thesestrains in food production are well documented.In particular, in recent years, great interest wasfocused on the possible use of certain productsof their metabolism, called bacteriocins, aspotential biopreservatives in foods (O’Sullivanet al. 2002). Bacteriocins are proteinaceous antimicrobialcompounds ribosomially synthesised by bacteriaand able to inhibit a high number of potentialpathogens among which Listeria monocytogenesand Staphylococcus aureus (Cotter et al. 2005). The current technologies employed to inacti-vate bacterial pathogens in foods are not alwaysefﬁcient and often represent particular treatmentsthat may modify the ﬁsical and chemical proper-ties of the food products. Therefore, newapproaches to combat pathogenic and spoilagemicroorganisms are needed. In the last fewyears, bacteriocins from LAB have been thor-oughly characterised and tested in food systemsas new food preservatives (Stiles 1996). Although many bacteriocins have been charac-terised, two of the most widely used in foodindustry as biopreservative are nisin (Class I,lantibiotic) and pediocin (Class II). Nisin is thebacteriocin with the longest history of safe usein food industry. It has been shown to be effec-tive for the microbial control in a number ofdairy products and also widely assessed incheese manufacturing (Ross et al. 2002). Inmost of cases, the bacteriocin is incorporatedinto the product as a dried concentrated powder(O’Sullivan et al. 2002), but currently, the useof nisin-producing starter or costarter culturesseems to be an alternative way of incorporatingthe bacteriocin (e.g. cheesemaking process)(Sobrino-Lopez and Marton-Belloso 2008). Among the pathogenic bacteria potentiallyassociated with dairy foods, S. aureus andL. monocytogenes are the cause of numerous
Unsupervised and Efficient Vocabulary Expansion for Recurrent Neural Network Language Models in ASR

In automatic speech recognition (ASR) systems, recurrent neural network language models (RNNLM) are used to rescore a word lattice or N-best hypotheses list. Due to the expensive training, the RNNLM's vocabulary set accommodates only small shortlist of most frequent words. This leads to suboptimal performance if an input speech contains many out-of-shortlist (OOS) words. An effective solution is to increase the shortlist size and retrain the entire network which is highly inefficient. Therefore, we propose an efficient method to expand the shortlist set of a pretrained RNNLM without incurring expensive retraining and using additional training data. Our method exploits the structure of RNNLM which can be decoupled into three parts: input projection layer, middle layers, and output projection layer. Specifically, our method expands the word embedding matrices in projection layers and keeps the middle layers unchanged. In this approach, the functionality of the pretrained RNNLM will be correctly maintained as long as OOS words are properly modeled in two embedding spaces. We propose to model the OOS words by borrowing linguistic knowledge from appropriate in-shortlist words. Additionally, we propose to generate the list of OOS words to expand vocabulary in unsupervised manner by automatically extracting them from ASR output.
Lack of association between rs 3807989 in cav 1 and atrial fibrillation

Background: A novel gene Caveolin-1(CAV1) was identified to be susceptibility to PR interval and also associated with atrial fibrillation (AF) in two Genome wide associations studies (GWAS) studies in European ancestry. The purpose of this study was to determine the association of the SNPs in CAV1 gene of rs3807989 with AF in Chinese Han patients. Methods and results: We attempted a replication in a cohort of 839 Chinese AF patients and 1215 healthy controls using melting temperature shift allele-specific genotyping analysis. One SNP in CAV1 (rs3807989) was genotyped. The final study cohort consisted of 839 AF patients and 1215 healthy controls. No significant association was detected between rs3807989 and AF in a Chinese Han population (allelic P-adj = 0.828 with OR = 1.02; genotypic P-adj = 0.815, 0.405, 0.760 with a dominant model, recessive model, and additive model). After logistic regression with multiple covariates, the association remained non-significant with adjusted P value 0.828. When the AF cases were further divided into lone AF (31.5%) and other types of AF (68.5%), no significant association was found between rs3807989 and lone AF (P-adj = 0.929 with OR = 0.990) and other types of AF (P-adj = 0.597 with OR = 1.060). Conclusion: The SNP rs3807989 in CAV1 gene is not associated with AF or lone AF in our studies, which suggests that the SNP rs3807989 in CAV1 may not be a risk factor for AF in Chinese Han population.