Miracle-dz/UniFAR-FTUs huggingface dataset:
What Can We Learn about Fall Risk Factors from EHR Nursing Notes? A Text Mining Study

Introduction: Hospital falls are a continuing clinical concern, with over one million falls occurring each year in the United States. Annually, hospital-acquired falls result in an estimated $34 billion in direct medical costs. Falls are considered largely preventable and, as a result, the Centers for Medicare and Medicaid Services have announced that fall-related injuries are no longer a reimbursable hospital cost. While policies and practices have been implemented to reduce falls, little sustained reduction has been achieved. Little empirical evidence supports the validity of published fall risk factors. While chart abstraction has been used to operationalize risk factors, few studies have examined registered nurses’ (RNs’) narrative notes as a source of actionable data. Therefore, the purpose of our study was to explore whether there is meaningful fall risk and prevention information in RNs’ electronic narrative notes. Methods: This study utilized a natural language processing design. Data for this study were extracted from the publicly available Medical Information Mart for Intensive Care (MIMIC-III) database. The date comprises deidentified EHR data associated with patients who stayed in critical care units between 2001 and 2012. Text mining procedures were performed on RN’s narrative notes following the traditional steps of knowledge discovery. Results: The corpus of data extracted from MIMIC-III database was comprised of 1,046,053 RNs’ notes from 36,583 unique patients. We identified 3,972 notes (0.4 percent) representing 1,789 (5 percent) patients with explicit documentation related to fall risk/prevention. Around 10 percent of the notes (103,685) from 23,025 patients mentioned intrinsic (patient-related) factors that have been theoretically associated with risk of falling. An additional 1,322 notes (0.1 percent) from 692 patients (2 percent) mentioned extrinsic risk factors, related to organizational design and environment. Moreover, 7672 notes (0.7 percent) from 2,571 patients (7 percent) included information on interventions that could theoretically impact patient falls. Conclusions: This exploratory study using a NLP approach revealed that meaningful information related to fall risk and prevention may be found in RNs’ narrative notes. In particular, RNs’ notes can contain information about clinical as well as environmental and organizational factors that could affect fall risk but are not explicitly recorded by the provider as a fall risk factors. In our study, potential fall risk factors were documented for more than half of the sample. Further research is needed to determine the predictive value of these factors. Implications for Policy or Practice: This study highlights a potentially rich but understudied source of actionable fall risk data. Furthermore, the application of novel methods to identify quality and safety measures in RNs’ notes can facilitate inclusion of RNs’ voices in patient outcomes and health services research.
Association of metformin administration with gut microbiome dysbiosis in healthy volunteers

Background Metformin is a widely used first-line drug for treatment of type 2 diabetes. Despite its advantages, metformin has variable therapeutic effects, contraindications, and side effects. Here, for the very first time, we investigate the short-term effect of metformin on the composition of healthy human gut microbiota. Methods We used an exploratory longitudinal study design in which the first sample from an individual was the control for further samples. Eighteen healthy individuals were treated with metformin (2 × 850 mg) for 7 days. Stool samples were collected at three time points: prior to administration, 24 hours and 7 days after metformin administration. Taxonomic composition of the gut microbiome was analyzed by massive parallel sequencing of 16S rRNA gene (V3 region). Results There was a significant reduction of inner diversity of gut microbiota observed already 24 hours after metformin administration. We observed an association between the severity of gastrointestinal side effects and the increase in relative abundance of common gut opportunistic pathogen Escherichia-Shigella spp. One week long treatment with metformin was associated with a significant decrease in the families Peptostreptococcaceae and Clostridiaceae_1 and four genera within these families. Conclusions Our results are in line with previous findings on the capability of metformin to influence gut microbiota. However, for the first time we provide evidence that metformin has an immediate effect on the gut microbiome in humans. It is likely that this effect results from the increase in abundance of opportunistic pathogens and further triggers the occurrence of side effects associated with the observed dysbiosis. An additional randomized controlled trial would be required in order to reach definitive conclusions, as this is an exploratory study without a placebo control arm. Our findings may be further used to create approaches that improve the tolerability of metformin.
Husbands’ knowledge and attendance at wives’ postpartum care among rural farmers

Abstract We examined husbands’ knowledge and attendance at their wives’ postpartum visit in a sample of rural husband-and-wife farmer dyads in central Malawi. A cross-sectional matched-pairs survey of 70 husband-and-wife farmer dyads, who lived in rural communities in Ntcheu district, and had a live birth in the past year was conducted. Data were collected using an interviewer-administered, structured postpartum questionnaire adapted from WHO Safe Motherhood Needs Assessment Questionnaires. Many husbands did not know about postpartum assessments and education their wives received from health facilities. Percent agreement between dyads’ responses was lower on questions referring to assessments than to education. The odds of reporting that the woman received postpartum assessments were greater among husbands than among wives. Fifty-nine percent of husbands did not go with their wives for 1-week postpartum visits. Top three reasons for not attending visits were: at work, out of town, and did not see the need.
Preventing and treating brain metastases with three first-line EGFR-tyrosine kinase inhibitors in patients with EGFR mutation-positive advanced non-small cell lung cancer

Introduction: Brain metastases (BM) are common in advanced non-small cell lung cancer (NSCLC), and the prognosis is poor with few therapeutic options. This study evaluated the efficacy of three epidermal growth factor receptor–tyrosine kinase inhibitors (EGFR-TKIs) in preventing and treating BM in patients with EGFR mutation-positive advanced NSCLC. Methods: Patients with EGFR mutation-positive advanced NSCLC who visited a tertiary referral center from 1 December 2013 to 30 November 2017 were analyzed retrospectively. They received gefitinib, erlotinib, or afatinib until disease progression, death, or intolerable adverse events. The cumulative incidence of subsequent BM of initial non-BM patients, progression-free survival (PFS), and overall survival (OS) of the BM and non-BM patients were estimated and compared using the Kaplan–Meier and log-rank tests. Results: 306 NSCLC patients were enrolled, with 116, 75, and 115 receiving first-line gefitinib, erlotinib, and afatinib, respectively. The afatinib group had a better PFS [12.7 versus 9.8 months; hazard ratio (HR) 0.59, p = 0.001] and OS (39.1 versus 22.0 months; HR 0.64, p = 0.035) than the gefitinib group. Afatinib tended to provide better BM prevention than gefitinib (BM cumulative incidence, HR 0.49; 95% confidence interval 0.34–0.71, p < 0.001) according to a Cox model adjusted for possible confounders. Patients with initial BM had a shorter PFS (p < 0.001) and OS (p = 0.015) than those without initial BM. Among the former, there were no differences in median PFS (p = 0.34) and median OS (p = 0.46) in the three EGFR-TKI groups. Conclusions: Our data suggested that, compared with gefitinib, afatinib provided better benefits significantly in terms of PFS and OS. Both had the same effectiveness in preventing subsequent BM.
Effect of Cold Stress on Photosynthetic Traits, Carbohydrates, Morphology, and Anatomy in Nine Cultivars of Stevia rebaudiana

Stevia rebaudiana Bertoni is a sweet medicinal herb that is cultivated worldwide. This study aimed to identify the genotypic responses and function of nine cultivars of S. rebaudiana (accession numbers 1–9 from the EUSTAS Stevia Gene Bank) to low temperature. Plants were grown in vitro and incubated under controlled conditions at 5° or 25°C for 1 month. Cold stress significantly decreased the maximum quantum yield of photosystem II (Fv/Fm) in all cultivars, which was more pronounced in cultivars 5, 6, 8, and 9. The efficiency of photosystems I and II (PIABS) also declined in cold-stressed plants and was accompanied by reductions in net photosynthesis (PN), intercellular CO2 (Ci), water use efficiency (WUE), and chlorophyll a, chlorophyll b and carotenoid contents, more so in cultivars 5, 6, 8, and 9. Regardless of the downregulation of photosynthetic capacity, the cold stress increased water-soluble carbohydrates in all cultivars, which was accompanied by an increase in fresh leaf mass and area, more so in cultivars 5, 6, 8, and 9. Furthermore, cold stress increased the stomatal index and density, epidermal cell density, stem diameter, xylem vessel width, phloem tissue width, and number of sclerenchyma in all cultivars. Even though the nine cultivars of S. rebaudiana had lower PSII efficiencies at low temperatures, the increase in carbohydrates and leaf mass suggests that damage to PSII is not responsible for the reduction in its efficiency.
Complexity on the Menu and in the Meal

Complexity is generally perceived to be a desirable attribute as far as the design/delivery of food and beverage experiences is concerned. However, that said, there are many different kinds of complexity, or at least people use the term when talking about quite different things, and not all of them are relevant to the design of food and drink experiences nor are they all necessarily perceptible within the tasting experience (either in the moment or over time). Consequently, the consumer often needs to infer the complexity of a tasting experience that is unlikely to be perceptible (in its entirety) in the moment. This paper outlines a number of different routes by which the chef, mixologist, and/or blender can both design and signal the complexity in the tasting experience.
Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom

How algae turn tides toxic Algal blooms can devastate marine mammal communities through the production of neurotoxins that accumulate within the food web. Brunson et al. identified a cluster of genes associated with biosynthesis of the neurotoxin domoic acid in a marine diatom (see the Perspective by Pohnert et al.). In vitro experiments established a series of enzymes that create the core structure of the toxin. Knowledge of the genes involved in domoic acid production will allow for genetic monitoring of algal blooms and aid in identifying conditions that trigger toxin production. Science, this issue p. 1356; see also p. 1308 Marine algae cluster genes involved in production of a toxin that causes neurological disorders. Oceanic harmful algal blooms of Pseudo-nitzschia diatoms produce the potent mammalian neurotoxin domoic acid (DA). Despite decades of research, the molecular basis for its biosynthesis is not known. By using growth conditions known to induce DA production in Pseudo-nitzschia multiseries, we implemented transcriptome sequencing in order to identify DA biosynthesis genes that colocalize in a genomic four-gene cluster. We biochemically investigated the recombinant DA biosynthetic enzymes and linked their mechanisms to the construction of DA’s diagnostic pyrrolidine skeleton, establishing a model for DA biosynthesis. Knowledge of the genetic basis for toxin production provides an orthogonal approach to bloom monitoring and enables study of environmental factors that drive oceanic DA production.
Niche partitioning of a pathogenic microbiome driven by chemical gradients

Chemical gradients shape the cystic fibrosis lung microbiome, with marked effects on the outcome of antimicrobial treatments. Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states.
Early weaning completely eliminates porcine cytomegalovirus from a newly established pig donor facility for xenotransplantation

For clinical xenotransplantation, transplants must be free of porcine cytomegalovirus (PCMV). Piglets become infected primarily in the perinatal period by the mother sow. While individual donor animals can be protected from infection by isolation husbandry, success is not guaranteed and this strategy poses the risk of undetected infections and raises animal welfare questions. Here, we present the establishment of a completely PCMV‐negative pig herd for breeding donor animals for xenotransplantation. Eleven pregnant DanAvl Basic hybrid sows were purchased from a designated pathogen‐free (DPF), PCMV‐positive colony and transferred to a new pig facility at the Centre for Innovative Medical Models (CiMM) 4 weeks prior to farrowing. At the age of 24 hours, piglets were early‐weaned and transferred to a commercially available Rescue Deck system dedicated to motherless rearing of piglets. Sows were removed from the facility. The PCMV status of F1‐generation animals was determined at regular intervals over a period of 14 months by a sensitive real‐time PCR‐based detection method testing blood, nasal swabs and cultured peripheral blood mononuclear cells (PBMCs). F1 sows were used as recipients of genetically modified embryos to generate a xenotransplant donor herd. Offspring were tested for PCMV accordingly. All offspring have remained PCMV negative over the whole observation period of 14 months. A completely PCMV‐negative pig herd for xenotransplantation has thus been successfully established.
Understanding Lignin Aggregation Processes. A Case Study: Budesonide Entrapment and Stimuli Controlled Release from Lignin Nanoparticles

The mechanism of lignin nanoprecipitation and subsequent self-assembly was elucidated by studying generation of lignin nanoparticles (LNPs) from aqueous ethanol. LNP formation was found to follow a kinetically controlled nucleation–growth mechanism in which large lignin molecules formed the initial critical nuclei. Using this information, we demonstrate entrapment of budesonide in LNPs and subsequent pH-triggered and surfactant-responsive release of this synthetic anti-inflammatory corticosteroid. Overall, our results not only provide a promising intestinal delivery system for budesonide but also deliver fundamental mechanistic understanding for the entrapment of actives in LNPs with controlled size and release properties.
Spotting review spammer groups: A cosine pattern and network based method

Nowadays, online product reviews strongly influence the purchase decision of consumers in e‐commerce platforms. Driven by the immense financial profits, review spammers deliberately post fake reviews to promote or demote their target products. Some spammers are even organized as groups to work together and try to take total control of the sentiment on their target products. To detect such spammer groups, most previous works exploit frequent itemset mining (FIM) to find spammer group candidates and then use unsupervised spamicity ranking methods to identify real spammer groups. However, these methods usually suffer from the problem of threshold setting, ie, high support value finding fewer groups while low support value leading to more coincidentally generated groups and computational inefficiency. Moreover, the unsupervised methods are not able to make good use of labeled instances which are actually obtainable in practice. In this paper, we propose CONSGD, a cosine pattern and heterogeneous information network–based spammer group detecting method. Specifically, the CONSGD uses cosine pattern mining (CPM) to discover tight spammer group candidates with a respective low support value, where the cosine threshold is utilized to avoid coincidentally generated groups. Moreover, CONSGD employs heterogeneous information network classification to identify the real spammer groups, which could utilize the labeled instances and do not rely to the assumption of independent instances. Experiments on real‐life dataset show that our proposed CONSGD is effective and outperforms the state‐of‐the‐art spammer group detection methods.
Collective behavior recognition using compact descriptors

This paper presents a novel hierarchical approach for collective behavior recognition based solely on ground-plane trajectories. In the first layer of our classifier, we introduce a novel feature called Personal Interaction Descriptor (PID), which combines the spatial distribution of a pair of pedestrians within a temporal window with a pyramidal representation of the relative speed to detect pairwise interactions. These interactions are then combined with higher level features related to the mean speed and shape formed by the pedestrians in the scene, generating a Collective Behavior Descriptor (CBD) that is used to identify collective behaviors in a second stage. In both layers, Random Forests were used as classifiers, since they allow features of different natures to be combined seamlessly. Our experimental results indicate that the proposed method achieves results on par with state of the art techniques with a better balance of class errors. Moreover, we show that our method can generalize well across different camera setups through cross-dataset experiments.
Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells

The true importance of cell-free DNA in human biology, together with the potential scale of its clinical utility, is tarnished by a lack of understanding of its composition and origin. In investigating the cell-free DNA present in the growth medium of cultured 143B cells, we previously demonstrated that the majority of cell-free DNA is neither a product of apoptosis nor necrosis. In the present study, we investigated the composition and origin of this cell-free DNA population using next-generation sequencing. We found that the cell-free DNA comprises mainly of repetitive DNA, including α-satellite DNA, mini satellites, and transposons that are currently active or exhibit the capacity to become reactivated. A significant portion of these cell-free DNA fragments originates from specific chromosomes, especially chromosomes 1 and 9. In healthy adult somatic cells, the centromeric and pericentromeric regions of these chromosomes are normally densely methylated. However, in many cancer types, these regions are preferentially hypomethylated. This can lead to double-stranded DNA breaks or it can directly impair the formation of proper kinetochore structures. This type of chromosomal instability is a precursor to the formation of nuclear anomalies, including lagging chromosomes and anaphase bridges. DNA fragments derived from these structures can recruit their own nuclear envelope and form secondary nuclear structures known as micronuclei, which can localize to the nuclear periphery and bud out from the membrane. We postulate that the majority of cell-free DNA present in the growth medium of cultured 143B cells originates from these micronuclei.
Epigenetically Silenced Candidate Tumor Suppressor Genes in Prostate Cancer: Identified by Modeling Methylation Stratification and Applied to Progression Prediction

Background: Recent studies have shown that epigenetic alterations, especially the hypermethylated promoters of tumor suppressor genes (TSGs), contribute to prostate cancer progression and metastasis. This article proposes a novel algorithm to identify epigenetically silenced TSGs (epi-TSGs) for prostate cancer. Methods: Our method is based on the perception that the promoter CpG island(s) of a typical epi-TSG has a stratified methylation profile over tumor samples. In other words, we assume that the methylation profile resembles the combination of a binary distribution of a driver mutation and a continuous distribution representing measurement noise and intratumor heterogeneity. Results: Applying the proposed algorithm and an existing method to The Cancer Genome Atlas prostate cancer data, we identify 57 candidate epi-TSGs. Over one third of these epi-TSGs have been reported to carry potential tumor suppression functions. The negative correlations between the expression levels and methylation levels of these genes are validated on external independent datasets. We further find that the expression profiling of these genes is a robust predictive signature for Gleason scores, with the AUC statistic ranging from 0.75 to 0.79. The identified signature also shows prediction strength for tumor progression stages, biochemical recurrences, and metastasis events. Conclusions: We propose a novel method for pinpointing candidate epi-TSGs in prostate cancer. The expression profiling of the identified epi-TSGs demonstrates significant prediction strength for tumor progression. Impact: The proposed epi-TSGs identification method can be adapted to other cancer types beyond prostate cancer. The identified clinically significant epi-TSGs would shed light on the carcinogenesis of prostate adenocarcinomas.
G Protein-Coupled Receptor Systems as Crucial Regulators of DNA Damage Response Processes

G protein-coupled receptors (GPCRs) and their associated proteins represent one of the most diverse cellular signaling systems involved in both physiological and pathophysiological processes. Aging represents perhaps the most complex biological process in humans and involves a progressive degradation of systemic integrity and physiological resilience. This is in part mediated by age-related aberrations in energy metabolism, mitochondrial function, protein folding and sorting, inflammatory activity and genomic stability. Indeed, an increased rate of unrepaired DNA damage is considered to be one of the ‘hallmarks’ of aging. Over the last two decades our appreciation of the complexity of GPCR signaling systems has expanded their functional signaling repertoire. One such example of this is the incipient role of GPCRs and GPCR-interacting proteins in DNA damage and repair mechanisms. Emerging data now suggest that GPCRs could function as stress sensors for intracellular damage, e.g., oxidative stress. Given this role of GPCRs in the DNA damage response process, coupled to the effective history of drug targeting of these receptors, this suggests that one important future activity of GPCR therapeutics is the rational control of DNA damage repair systems.
Different‐shaped curves for serum uric acid with and without diabetes: Results from China Health and Retirement Longitudinal Study

Several studies have revealed conflicting results regarding the relationship between serum uric acid (SUA) and blood glucose concentrations. The aim of this study was to identify the shape of the curve between SUA and either fasting plasma glucose (FPG) or HbA1c in diabetic and non‐diabetic participants.