Miracle-dz/UniFAR-FTUs huggingface dataset:
CANCROX: a cross-species cancer therapy database

Abstract Cancer comprises a set of more than 200 diseases resulting from the uncontrolled growth of cells that invade tissues and organs, which can spread to other regions of the body. The types of cancer found in humans are also described in animal models, a fact that has raised the interest of the scientific community in comparative oncology studies. In this study, bioinformatics tools were used to implement a computational model that uses text mining and natural language processing to construct a reference database that relates human and canine genes potentially associated with cancer, defining genetic pathways and information about cancer and cancer therapies. The CANCROX reference database was constructed by processing the scientific literature and lists more than 1300 drugs and therapies used to treat cancer, in addition to over 10 000 combinations of these drugs, including 40 types of cancer. A user-friendly interface was developed that enables researchers to search for different types of information about therapies, drug combinations, genes and types of cancer. In addition, data visualization tools allow to explore and relate different drugs and therapies for the treatment of cancer, providing information for groups studying animal models, in this case the dog, as well as groups studying cancer in humans.
Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains

(1) Background: Processivity is common among enzymes and mechanochemical motors that synthesize, degrade, modify or move along polymeric substrates, such as DNA, RNA, polysaccharides or proteins. Processive enzymes can make multiple rounds of modification without releasing the substrate/partner, making their operation extremely effective and economical. The molecular mechanism of processivity is rather well understood in cases when the enzyme structurally confines the substrate, such as the DNA replication factor PCNA, and also when ATP energy is used to confine the succession of molecular events, such as with mechanochemical motors. Processivity may also result from the kinetic bias of binding imposed by spatial confinement of two binding elements connected by an intrinsically disordered (ID) linker. (2) Method: By statistical physical modeling, we show that this arrangement results in processive systems, in which the linker ensures an optimized effective concentration around novel binding site(s), favoring rebinding over full release of the polymeric partner. (3) Results: By analyzing 12 such proteins, such as cellulase, and RNAse-H, we illustrate that in these proteins linker length and flexibility, and the kinetic parameters of binding elements, are fine-tuned for optimizing processivity. We also report a conservation of structural disorder, special amino acid composition of linkers, and the correlation of their length with step size. (4) Conclusion: These observations suggest a unique type of entropic chain function of ID proteins, that may impart functional advantages on diverse enzymes in a variety of biological contexts.
Applying probabilistic latent semantic analysis to multi-criteria recommender system

Nowadays some recommender system researchers have already been engaging multi-criteria that model possible attributes of the item to generate the improved recommendations. However, the statistical machine learning methods successful in the single-rating recommender system have not been investigated in the context of multi-criteria ratings. In this paper, we propose two types of multi-criteria probabilistic latent semantic analysis algorithms extended from the single-rating version. First, the mixture of multi-variate Gaussian distribution is assumed to be the underlying distribution of multi-criteria ratings of each user. Second, we further assume the mixture of the linear Gaussian regression model as the underlying distribution of multi-criteria ratings of each user, inspired by the Bayesian network and linear regression. The experiment results on the Yahoo! Movies ratings data set show that the full multi-variate Gaussian model and the linear Gaussian regression model achieve a stable performance gain over other tested methods.
Relational Collaborative Filtering: Modeling Multiple Item Relations for Recommendation

Existing item-based collaborative filtering (ICF) methods leverage only the relation of collaborative similarity - i.e., the item similarity evidenced by user interactions like ratings and purchases. Nevertheless, there exist multiple relations between items in real-world scenarios, e.g., two movies share the same director, two products complement with each other, etc. Distinct from the collaborative similarity that implies co-interact patterns from the user's perspective, these relations reveal fine-grained knowledge on items from different perspectives of meta-data, functionality, etc. However, how to incorporate multiple item relations is less explored in recommendation research. In this work, we propose Relational Collaborative Filtering (RCF) to exploit multiple item relations in recommender systems. We find that both the relation type (e.g., shared director) and the relation value (e.g., Steven Spielberg) are crucial in inferring user preference. To this end, we develop a two-level hierarchical attention mechanism to model user preference - the first-level attention discriminates which types of relations are more important, and the second-level attention considers the specific relation values to estimate the contribution of a historical item. To make the item embeddings be reflective of the relational structure between items, we further formulate a task to preserve the item relations, and jointly train it with user preference modeling. Empirical results on two real datasets demonstrate the strong performance of RCF1. Furthermore, we also conduct qualitative analyses to show the benefits of explanations brought by RCF's modeling of multiple item relations.
Criteria, Procedures, and Future Prospects of Involuntary Treatment in Psychiatry Around the World: A Narrative Review

The use of involuntary treatments in psychiatry comes with some benefits and many disadvantages for the patient’s experience and the therapeutic outcome. This review proposes to compare the procedures and criteria for involuntary psychiatric treatment and to outline the current situation concerning the relevant legislation and practices around the world. Various historical and present-day criteria and procedures are described and compared, showing a certain degree of heterogeneity to this day. Studies relating to patient experiences of coercive measures and their effects on the therapeutic relationship and continued adherence are examined. The breach of the principle of self-determination appears as a central element of the critique; underlined both in clinical reality and in jurisprudence. Moreover, assessment of the patient's decision-making capacity regarding their own care, the use of advance treatment directives, and the reduction of the mental patient's stigma in favour of greater social and therapeutic support appear important. We highlight the similarities and differences between legislation and practice in various parts of Europe, North America, Asia, and some areas of Latin America, Africa and the South Pacific. Other aspects that we explored include the patient’s experience of coercion; the repercussions on the therapeutic relationship and adherence to treatment following coercion; the role it plays in the prevention of suicide; ethical problems; and possible alternatives to reduce the use of coercive measures.
The Effect of Auricular Plaster Therapy on Insomnia in Patients with Rheumatoid Arthritis.

Objective: This research was conducted to observe the effects of auricular plaster therapy on insomnia in patients with rheumatoid arthritis (RA). Materials and Methods: This study involved 76 patients with insomnia caused by RA, who were admitted to Foshan Chancheng Central Hospital-in Foshan, Guangdong, China-from August 2017 to August 2018. The patients were randomized, with 38 to the intervention group and another 38 to the control group. The intervention group was treated with auricular plaster therapy with beans, while the control group was treated with estazolam orally before going to bed. Curative effects were compared between the 2 groups. The Pittsburgh Sleep Quality Index scale (PSQI) and the Athens Insomnia Scale (AIS) were used to assess and evaluate the sleep quality of patients. Result: Scores of the PSQI dimensions all fell in both groups after treatment. Scores for sleep quality, sleep latency, sleep efficiency, sleep disorder, and daytime dysfunction in the observation group were lower than those in the control group (P < 0.05). AIS scores in all dimensions decreased in both groups, and, after treatment, scores and total points of sleep latency, night-time revival, overall sleep quality, and the dimensionality of daytime body function in the intervention group were lower than those in the control group (P < 0.05). Conclusions: Auricular plaster therapy has a marked effect on insomnia in patients with RA, and the therapy is easy and simple to apply.
On Lebesgue null sets

Letting A be a Borel subset of n dimensional Euclidean space, and W(x) be an m dimensional affine subspace containing x and varying in a Lipschitz way according to x, we establish that A is Lebesgue null if and only if $A \cap W(x)$ has m dimensional Hausdorff measure vanishing for almost every x.
Association between human leucocyte antigen-DO polymorphisms and interferon/ribavirin treatment response in hepatitis C virus type 1 infection in Chinese population: a prospective study

Objective The human leucocyte antigen-DO (HLA-DO) gene located in the HLA non-classical class-II region may play a role in treatment response to hepatitis C virus (HCV). This study was conducted to explore the role of single nucleotide polymorphisms (SNPs) in HLA-DO in responding to HCV therapy. Setting All patients were recruited between January 2011 and September 2016 from the Jurong People’s Hospital, Jiangsu Province, China. Participants A total of 346 chronic hepatitis C (CHC) patients who finished the 48-week pegylated interferon-alpha and ribavirin (PEG IFN-α/RBV) treatment were enrolled in this study. All patients were former remunerated blood donors. The inclusion criteria for patients were as follows: (1) treatment-naive and treated with PEG IFN-α/RBV, (2) HCV RNA was present in serum for over 6 months before treatment, (3) negative for hepatitis B (HBV) or HIV infection and (4) lacked any other hepatic diseases. All participants in this study were Chinese Han population and infected with HCV genotype 1b and treated with subcutaneous PEG IFN-α at a dose of 180 µg once a week with the addition of 800–1000 mg/d RBV according to weight orally for 48 weeks. Results The SNPs HLA-DOA rs1044429 and HLA-DOB rs2284191 and rs2856997 of 18 SNPs were correlated with HCV treatment response in the Chinese Han population. The dominant model indicated that patients carrying favourable genotypes at rs1044429 AA and rs2284191 AA were more likely to achieve sustained virological response (SVR) (OR 1.99, 95% CI 1.25 to 3.19; OR 2.71, 95% CI 1.58 to 4.63, respectively), while patients carrying unfavourable genotypes at rs2856997 GG were less likely to achieve SVR (OR 0.48, 95% CI 0.29 to 0.78). Conclusion Genetic variations at rs1044429, rs2284191 and rs2856997 were independent predictors of HCV treatment response in the Chinese Han population.
PlantMP: a database for moonlighting plant proteins

Abstract Moonlighting proteins are single polypeptide chains capable of executing two or more distinct biochemical and/or biological functions. Here, we describe the development of PlantMP, which is a manually curated online-based database of plant proteins that are known to `moonlight’. The database contains searchable UniProt IDs and names, canonical and moonlighting functions, gene ontology numbers, plant species as well as links to the PubMed indexed articles. Proteins homologous to experimentally confirmed moonlighting proteins from the model plant Arabidopsis thaliana are provided as a separate list of `likely moonlighters’. Additionally, we also provide a list of predicted Arabidopsis moonlighting proteins reported in the literature. Currently, PlantMP contains 110 plant moonlighting proteins, 10 `likely moonlighters’ and 27 `predicted moonlighters’. Organizing plant moonlighting proteins in one platform enables researchers to conveniently harvest plant-specific raw and processed data such as the molecular functions, biological roles and structural features essential for hypothesis formulation in basic research and for biotechnological innovations.
Ice and anti-nucleating activities of an ice-binding protein from the annual grass, Brachypodium distachyon.

Plants exposed to sub-zero temperatures face unique challenges that threaten their survival. The growth of ice crystals in the extracellular space can cause cellular dehydration, plasma membrane rupture and eventual cell death. Additionally, some pathogenic bacteria cause tissue damage by initiating ice crystal growth at high sub-zero temperatures through the use of ice-nucleating proteins (INPs), presumably to access nutrients from lysed cells. An annual species of brome grass, Brachypodium distachyon (Bd), produces an ice-binding protein (IBP) that shapes ice with a modest depression of the freezing point (~0.1 °C at 1 mg/mL), but high ice-recrystallization inhibition (IRI) activity, allowing ice crystals to remain small at near melting temperatures. This IBP, known as BdIRI, is unlike other characterized IBPs with a single ice-binding face, as mutational analysis indicates that BdIRI adsorbs to ice on two faces. BdIRI also dramatically attenuates the nucleation of ice by bacterial INPs (up to -2.26 °C). This 'anti-nucleating' activity is significantly higher than previously documented for any IBP.
Clinical and Experimental Gastroenterology Dovepress Fecal Microbiota Transplantation: Current Clinical Efficacy and Future Prospects

Fecal microbiota transplantation (FMT) has gained mainstream attention with its remarkable efficacy in treating recurrent Clostridium difficile infection (RCDI) when there are no other effective therapies. Methods of selecting donors and routes of administration vary among studies, but there are now randomized controlled trials showing efficacy of FMT in treating RCDI. Ongoing trials of FMT for other disease such as inflammatory bowel disease are underway; this therapy should not be used for these conditions unless there is strong evidence for efficacy. Long-term safety data are sorely needed, as well as clarification of regulatory concerns.
Ideal Cardiovascular Health and Adiposity: Implications in Youth

Background The American Heart Association set 2020 Strategic Impact Goals that defined cardiovascular risk factors to be included in the concept of ideal cardiovascular health (ICH). The prevalence of ICH among differing levels of adiposity in youth, especially severe obesity, is uncertain. Methods and Results The cross‐sectional study measured ICH metrics in 300 children and adolescents stratified by adiposity: normal weight, overweight/obese, and severely obese. ICH incorporates 7 behavioral and health metrics, and was characterized as poor, intermediate, or ideal. Individual ICH metrics were transformed into standardized sample z‐scores; a summary ICH sample z‐score was also calculated. Multivariable linear regression models were used to estimate differences in ICH sample z‐scores by adiposity status. Of the 300 participants, 113 were classified as having normal weight, 87 as having overweight/obesity, and 100 as having severe obesity (mean age 12.8 years, SD 2.7; 48% female). No participants met the criteria for ICH; 80% of those classified as having normal weight, 81% of those with overweight/obesity, and all of those with severe obesity were in poor cardiovascular health. After multivariable adjustment, those with overweight/obesity (sample z‐score: −1.35; 95% confidence interval, −2.3, −1.1) and severe obesity (sample z‐score: −1.45; 95% confidence interval, −2.9, −0.92) had lower overall ICH sample z‐scores compared with participants with normal weight. Results were similar for individual ICH metrics. Conclusions Poor cardiovascular health was highly prevalent in youth; ICH sample z‐scores increased across levels of adiposity. Youth with obesity, particularly those with severe obesity, remain a rich target for primary prevention efforts. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT01508598.
Differences in Cardiovascular Health Metrics in Emergency Medical Technicians Compared to Paramedics: A Cross-Sectional Study of Emergency Medical Services Professionals

Abstract Background: Emergency Medical Services (EMS) professionals face high physical demands in high-stress settings; however, the prevalence of cardiovascular health (CVH) risk factors in this health care workforce has not been explored. The primary objective of this study was to compare the distribution of CVH and its individual components between a sample of emergency medical technicians (EMTs) and paramedics. The secondary objective was to identify associations between demographic and employment characteristics with ideal CVH in EMS professionals. Methods: A cross-sectional survey based on the American Heart Association’s (AHA; Dallas, Texas USA) Life’s Simple 7 (LS7) was administered to nationally-certified EMTs and paramedics. The LS7 components were scored according to previously described cut points (ideal = 2; intermediate = 1; poor = 0). A composite CVH score (0-10) was calculated from the component scores, excluding cholesterol and blood glucose due to missing data. Multivariable logistic regression was used to estimate odds ratios (OR; 95% CI) for demographic and employment characteristics associated with optimal CVH (≥7 points). Results: There were 24,708 respondents that were currently practicing and included. More EMTs achieved optimal CVH (n = 4,889; 48.8%) compared to paramedics (n = 4,338; 40.6%). Factors associated with higher odds of optimal CVH included: higher education level (eg, college graduate or more: OR = 2.26; 95% CI, 1.97-2.59); higher personal income (OR = 1.26; 95% CI, 1.17-1.37); and working in an urban versus rural area (OR = 1.31; 95% CI, 1.23-1.40). Paramedic certification level (OR = 0.84; 95% CI, 0.78-0.91), older age (eg, 50 years or older: OR = 0.65; 95% CI, 0.58-0.73), male sex (OR = 0.54; 95% CI, 0.50-0.56), working for a non-fire-based agency (eg, private service: OR = 0.68; 95% CI, 0.62-0.74), and providing medical transport service (OR = 0.81; 95% CI, 0.69-0.94) were associated with lower odds of optimal CVH. Conclusions: Several EMS-related characteristics were associated with lower odds of optimal CVH. Future studies should focus on better understanding the CVH and metabolic risk profiles for EMS professionals and their association with incident cardiovascular disease (CVD), major cardiac events, and occupational mortality. Cash RE, Crowe RP, Bower JK, Foraker RE, Panchal AR. Differences in cardiovascular health metrics in emergency medical technicians compared to paramedics: a crosssectional study of Emergency Medical Services professionals. Prehosp Disaster Med. 2019;34(3):288–296.
Gain-of-Function STAT1 Mutation With Familial Lymphadenopathy and Hodgkin Lymphoma

In this report, we describe a novel T437N STAT1 mutation found in a mother and 3 of her 4 children which we demonstrate yields gain-of-function. All of the four patients with the T437N STAT1 mutation experienced lymphadenopathy. However, two of the children developed Nodular Lymphocyte Predominant Hodgkin Lymphoma (NHLPL) and have responded to chemotherapeutic regimens. The fourth sibling had neither the STAT1 variant nor lymphadenopathy or malignancy. To our knowledge this is the first description of a potential association between STAT1 GOF mutations and lymphoma development.
Community Detection in Hypergraphs: Optimal Statistical Limit and Efficient Algorithms

In this paper, community detection in hypergraphs is explored. Under a generative hypergraph model called “d-wise hypergraph stochastic block model” (d-hSBM) which naturally extends the Stochastic Block Model (SBM) from graphs to d-uniform hypergraphs, the fundamental limit on the asymptotic minimax misclassified ratio is characterized. For proving the achievability, we propose a two-step polynomial time algorithm that provably achieves the fundamental limit in the sparse hypergraph regime. For proving the optimality, the lower bound of the minimax risk is set by finding a smaller parameter space which contains the most dominant error events, inspired by the analysis in the achievability part. It turns out that the minimax risk decays exponentially fast to zero as the number of nodes tends to infinity, and the rate function is a weighted combination of several divergence terms, each of which is the Rényi divergence of order 1/2 between two Bernoulli distributions. The Bernoulli distributions involved in the characterization of the rate function are those governing the random instantiation of hyperedges in d-hSBM. Experimental results on both synthetic and real-world data validate our theoretical finding.
Great Expectations? Relation of Previous Experiences With Social Robots in Real Life or in the Media and Expectancies Based on Qualitative and Quantitative Assessment

Social robots, which mostly look and behave like humans, are often perceived as somehow alive and treated similar to humans, despite the fact that they are non-living electronic devices. Based on considerations of the uncertainty reduction theory, the question arises what expectancies regarding social robots people have and what sources they use to achieve these expectancies. To receive an in-depth understanding of people’s expectancies regarding social robots and particularly how these expectancies are influenced by people’s experiences with real robots but also with fictional robots from media, thirteen semi-structured interviews and a quantitative online study (n = 433) were conducted. Results indicate that people’s experiences with robots in the media lead to high expectations regarding the skills of robots, which in turn increase people’s general expectancies regarding social robots being part of the society as well as their personal lives. Furthermore, knowledge of negatively perceived fictional robots increases negative expectancies of robots becoming a threat to humans, while technical affinity reduces general robot anxiety.
Ovary-sparing surgery for benign pediatric ovarian masses.

PURPOSE OF REVIEW This review highlights progress in the management of pediatric ovarian neoplasms. Recent research has identified disparities in the management of patients with benign ovarian neoplasms based on a variety of factors. However, the long-term effects of unilateral oophorectomy have prompted an emphasis on ovary-sparing surgery (OSS) for benign masses. One of the challenges still facing providers is the preoperative differentiation between benign and malignant masses. RECENT FINDINGS Recent studies highlight the variability in practice patterns surrounding the management of benign ovarian neoplasms. Progress continues to be made in identifying reliable factors that can be used to inform preoperative risk stratification of patients who present with ovarian neoplasms. These factors include imaging characteristics, symptoms and tumor markers. In addition, the safety of OSS with regard to recurrence and upstaging in appropriate settings continues to be demonstrated. SUMMARY This review highlights the importance of multidisciplinary collaboration in the treatment of ovarian neoplasms given the varied surgical approach by specialty. Multiple retrospective studies have identified factors that can be used for preoperative risk stratification and selection of patients for OSS. Prospective studies evaluating the accuracy of these factors for preoperative risk stratification are needed.