Miracle-dz/UniFAR-FTUs huggingface dataset:
A point-process matched filter for event detection and decoding from population spike trains

Objective. Information encoding in neurons can be described through their response fields. The spatial response field of a neuron is the region of space in which a sensory stimulus or a behavioral event causes that neuron to fire. Neurons can also exhibit temporal response fields (TRFs), which characterize a transient response to stimulus or behavioral event onsets. These neurons can thus be described by a spatio-temporal response field (STRF). The activity of neurons with STRFs can be well-described with point process models that characterize binary spike trains with an instantaneous firing rate that is a function of both time and space. However, developing decoders for point process models of neurons that exhibit TRFs is challenging because it requires prior knowledge of event onset times, which are unknown. Indeed, point process filters (PPF) to date have largely focused on decoding neuronal activity without considering TRFs. Also, neural classifiers have required data to be behavior- or stimulus-aligned, i.e. event times to be known, which is often not possible in real-world applications. Our objective in this work is to develop a viable decoder for neurons with STRFs when event times are unknown. Approach. To enable decoding of neurons with STRFs, we develop a novel point-process matched filter (PPMF) that can detect events and estimate their onset times from population spike trains. We also devise a PPF for neurons with transient responses as characterized by STRFs. When neurons exhibit STRFs and event times are unknown, the PPMF can be combined with the PPF or with discrete classifiers for continuous and discrete brain state decoding, respectively. Main results. We validate our algorithm on two datasets: simulated spikes from neurons that encode visual saliency in response to stimuli, and prefrontal spikes recorded in a monkey performing a delayed-saccade task. We show that the PPMF can estimate the stimulus times and saccade times accurately. Further, the PPMF combined with the PPF can decode visual saliency maps without knowing the stimulus times. Similarly, the PPMF combined with a point process classifier can decode the saccade direction without knowing the saccade times. Significance. These event detection and decoding algorithms can help develop neurotechnologies to decode cognitive states from neural responses that exhibit STRFs.
The Use of HPLC-PDA in Determining Nicotine and Nicotine-Related Alkaloids from E-Liquids: A Comparison of Five E-Liquid Brands Purchased Locally

E-liquid manufacturers are under scrutiny concerning the purity and concentration accuracy of nicotine and the minor nicotine-related alkaloids (NRAs) packaged in their products. In this communication we report concentrations of nicotine and five NRAs (nornicotine, cotinine, anabasine, anatabine, myosmine) from locally purchased E-liquids. Methods: Five brands of E-liquids (three bottles each) were purchased locally. Additionally, three bottles of reference E-liquid were prepared. Concentrations of nicotine and NRAs from each bottle were measured by HPLC. Concentrations of these alkaloids were also determined from electronic cigarette-generated aerosol and traditional cigarette smoke. Results: Nicotine concentrations in E-liquid brands 1, 2, 3, 4, 5 and in the reference E-liquid were 17.8 ± 4.1, 23.2 ± 0.7, 24.0 ± 0.9, 24.9 ± 0.2, 19.7 ± 0.3 and 20.4 ± 0.1 mg/mL, respectively. Concentrations normalized to 100% of product label were 74%, 97%, 100%, 104%, 109% and 102%, respectively. E-liquid brand 1 showed significance (p < 0.001) between bottles, while the reference showed the least variability. Similar results were obtained for the NRAs. Results also indicated the NRAs in aerosol of the reference E-liquid are lower than in cigarette smoke. Conclusions: The amounts of NRAs present in E-liquids and E-liquid aerosol are less compared to cigarettes, however, inconsistencies and variation in nicotine concentrations supports the need for regulatory oversight.
Using Electronic Health Records and Machine Learning to Predict Postpartum Depression

Postpartum depression (PPD) is one of the most frequent maternal morbidities after delivery with serious implications. Currently, there is a lack of effective screening strategies and high-quality clinical trials. The ability to leverage a large amount of detailed patient data from electronic health records (EHRs) to predict PPD could enable the implementation of effective clinical decision support interventions. To develop a PPD prediction model, using EHRs from Weill Cornell Medicine and NewYork-Presbyterian Hospital between 2015-17, 9,980 episodes of pregnancy were identified. Six machine learning algorithms, including L2-regularized Logistic Regression, Support Vector Machine, Decision Tree, Naïve Bayes, XGBoost, and Random forest were constructed. Our model's best prediction performance achieved an AUC of 0.79. Race, obesity, anxiety, depression, different types of pain, antidepressants, and anti-inflammatory drugs during pregnancy were among the significant predictors. Our results suggest a potential for applying machine learning to EHR data to predict PPD and inform healthcare delivery.
Efficacy of oxycodone in intravenous patient-controlled analgesia with different infusion modes after laparoscopic radical surgery of cervical cancer a prospective, randomized, double-blind study

Abstract Backgroud: The aim of this study was to compare the analgesic and adverse effects of oxycodone with 3 different infusion modes on postoperative pain after laparoscopic radical surgery of cervical cancer. Methods: Ninety patients undergoing laparoscopic radical surgery of cervical cancer were randomly divided into 3 groups: Group A (continuous infusion with 0.01 mg/kg/h and a bolus dose with 0.03 mg/kg), Group B (a bolus dose with 0.03 mg/kg) and Group C (PCA was administered as a time-scheduled decremental continuous infusion based on lean body mass). A blinded observer recorded Visual Analogue Scale (VAS), Ramsay sedation score (RSS), infused cumulative dose of oxycodone and side effects at 1, 6, 12, 24, and 48 hours postoperatively, and satisfaction during the postoperative 48 hours. Results: There were significant differences in the VAS pain score when resting or coughing among 3 groups at 1, 6 and 48 hours postoperatively (P <.05). VAS was significantly higher in Group B than in Group A and C until postoperative 1, 6, and 48 hours (P <.05). There were significant differences in cumulative PCA dose among the 3 groups at 1 and 48 hours postoperatively (P <.05). Group C showed significantly less amount of cumulative PCA dose compared to other 2 groups at 1 hour, whereas cumulative PCA dose of Group A at 48 hours was significantly more than other 2 groups (P <.05). There were no significant differences in postoperative nausea and vomiting, FAS, muscle chilling score and RSS among 3 groups at 1, 6, 12, 24 and 48 hours postoperatively. In addition, there was no difference in overall satisfaction during 48 hours postoperatively among 3 groups. Conclusions: Oxycodone provides significant analgesic effect in 3 different infusion modes over 48 hours after laparoscopic radical surgery of cervical cancer, and a time-scheduled decremental continuous infusion of oxycodone can become a better choice for patients after surgery of cervical cancer.
Incorporating molecular biomarkers into clinical practice for gastric cancer

ABSTRACT Introduction: Gastric cancer is one of the most common causes of cancer-related mortality worldwide. To improve clinical outcomes, it is critical to develop appropriate approaches to diagnosis and treatment. Biomarkers have numerous potential clinical applications, including screening, assessing risk, determining prognosis, monitoring recurrence, and predicting response to treatment. Furthermore, biomarkers may contribute to the development of effective therapies. Areas covered: Here we review recent progress in exploiting GC-specific biomarkers such as protein-coding genes, microRNAs, long noncoding RNAs, and methylated gene promoters. Expert opinion: The development of biomarkers for diagnosing and monitoring gastric cancer and for individualizing therapeutic targets shows great promise for improving gastric cancer management.
Predictors of Number of Healthcare Professionals Consulted by Individuals with Mental Disorders or High Psychological Distress

This study assesses the contribution of predisposing, enabling, and needs factors and related variables that predicted the number of healthcare professionals consulted for mental health reasons among 746 individuals with mental disorders and high psychological distress. The data were drawn from the third (T3) and fourth data collection periods (T4) of a longitudinal study conducted in a Quebec/Canada epidemiological catchment area. Hierarchical linear regression was performed on the number of types of healthcare professionals consulted in the 12 months prior to T4. Predictors were identified at T3, classified as predisposing, enabling, and needs factors (i.e., clinical and related variables) according to the Andersen Behavioral Model. Three needs factors were associated with the number of types of healthcare professionals consulted: Post-traumatic stress disorder, stressful events, and marginally suicide ideation. Three enabling factors: Having a family physician, previous use of mental health services, and employment status were also related to the dependent variable. Poor self-perception of mental health status was the only predisposing factor retained. While needs factors were the main predictors of the number of types of healthcare professionals consulted, enabling factors may reduce the influence of needs factors, by the deployment of various strategies that facilitate continuous and appropriate care.
Pregnancy as a transition: First‐time expectant couples′ experience with alcohol consumption

Abstract Introduction and Aims Most official healthcare guidelines apply the precautionary principle by recommending that pregnant women abstain from any alcohol consumption. However, a number of women continue drinking alcohol while pregnant. The aim of this study was to investigate couples′ experiences of the issue of alcohol consumption during pregnancy as a transitional process. Design and Methods Thirty semi‐directive joint interviews were conducted with couples expecting their first child in Switzerland. Interviews were analysed thematically with the help of ATLAS.ti. Results Couples endorsed the imperative of changing drinking habits and all the women reduced their alcohol consumption, although some reported difficulties. First, we identified three themes describing how couples experienced the woman′s change of drinking habits as a smooth transition: Internalisation of risk discourses, abstinence as a social norm and embodiment of alcohol aversion. Second, we emphasised four kinds of difficulties that couples encountered in their everyday lives: burden of risk discourses, conflicting advice, social occasions and desire for alcohol. Discussion and Conclusions This paper makes a significant contribution by examining prenatal drinking change as a transition. In this conceptualisation, the change of alcohol consumption is a relational process that is shaped by multiple changes and social norms. Our findings have important implications for practice. First, health professionals should be aware of the difficulties women experience when they abstain from alcohol during pregnancy. Second, our findings suggest the importance of a patient‐centred approach that considers the role of the partner in supporting a pregnant woman′s change of alcohol consumption.
A Systematic Review On Synthetic Drugs And Phytopharmaceuticals Used To Manage Diabetes.

BACKGROUND Diabetes is a multifactorial disease and a major cause for many microvascular and macrovascular complications. The disease will ultimately lead to high rate mortality if it is not managed properly. Treatment of diabetes without any side effects has always remained a major challenge for the health care practitioners. INTRODUCTION The current review discusses the various conventional drugs, herbal drugs, combination therapy and the use of nutraceuticals for the effective management of diabetes mellitus. The biotechnological aspects of various antidiabetic drugs are also discussed. METHODS Structured search of bibliographic databases for previously published peer-reviewed research papers was explored and data was culminated in terms of various approaches that are used for the treatment of diabetes. RESULTS More than 170 papers including both, research and review articles, were included in this review in order to produce a comprehensive as well as readily understandable article. A series of herbal and synthetic drugs have been discussed along with their current status of treatment in terms of dose, mechanism of action and possible side effects. The article also focuses on combination therapies containing synthetic as well as herbal drugs to treat the disease. The role of pre and probiotics in management of diabetes is also highlighted. CONCLUSION Oral antihyperglycemics which are used to treat diabetes can cause many adverse effects and if given in combination can lead to drug-drug interactions. The combination of various phytochemicals with synthetic drugs can overcome the challenge faced by the synthetic drug treatment. Herbal and nutraceuticals therapy and the use of probiotics and prebiotics is a more holistic therapy due to its natural origin and traditional use.
Diagnosis and Management of Left Atrium Appendage Thrombosis in Atrial Fibrillation Patients Undergoing Cardioversion

Atrial fibrillation is the most common cardiac arrhythmia and is associated with an increased risk of stroke and thromboembolic complications. A rhythm control strategy with both electrical and pharmacological cardioversion is recommended for patients with symptomatic atrial fibrillation. Anticoagulant therapy for 3–4 weeks prior to cardioversion is recommended in order to avoid thromboembolic events deriving from restoring sinus rhythm. Transesophageal echocardiography has a pivotal role in this setting, excluding the presence of left atrial appendage thrombus before cardioversion. The aim of this review is to discuss the epidemiology and risk factors for left atrial appendage thrombosis, the role of echocardiography in the decision making before cardioversion, and the efficacy of different anticoagulant regimens on the detection and treatment of left atrial appendage thrombosis.
C9ORF72-related cellular pathology in skeletal myocytes derived from ALS-patient induced pluripotent stem cells

ABSTRACT Amyotrophic lateral sclerosis (ALS) is a late-onset neuromuscular disease with no cure and limited treatment options. Patients experience a gradual paralysis leading to death from respiratory complications on average only 2-5 years after diagnosis. There is increasing evidence that skeletal muscle is affected early in the disease process, yet the pathological processes occurring in the skeletal muscle of ALS patients are still mostly unknown. Specifically, the most common genetic cause of ALS, a hexanucleotide repeat expansion in the C9ORF72 gene, has yet to be fully characterized in the context of skeletal muscle. In this study, we used the protocol previously developed in our lab to differentiate skeletal myocytes from induced pluripotent stem cells (iPSCs) of C9ORF72 ALS (C9-ALS) patients in order to create an in vitro disease model of C9-ALS skeletal muscle pathology. Of the three C9ORF72 mutation hallmarks, we did not see any evidence of haploinsufficiency, but we did detect RNA foci and dipeptide repeat (DPR) proteins. Additional abnormalities included changes in the expression of mitochondrial genes and a susceptibility to oxidative stress, indicating that mitochondrial dysfunction may be a critical feature of C9-ALS skeletal muscle pathology. Finally, the C9-ALS myocytes had increased expression and aggregation of TDP-43. Together, these data show that skeletal muscle cells experience pathological changes due to the C9ORF72 mutation. Our in vitro model could facilitate further study of cellular and molecular pathology in ALS skeletal muscle in order to discover new therapeutic targets against this devastating disease. This article has an associated First Person interview with the first author of the paper. Summary: Evidence of protein aggregation and mitochondrial dysfunction were found in skeletal myocytes differentiated from ALS-patient induced pluripotent stem cells with the C9ORF72 mutation.
Environmental Toxicology and Chemistry

A study was performed to evaluate the potential biological impacts from 8 different miscellaneous discharges from an oil and gas mobile offshore drilling unit (MODU) including deck drainage, desalination unit waste, boiler blowdown, fire control system test water, noncontact cooling water, and bilge water. Samples were evaluated for toxicity using a rapid (<1 h) initial screening test (echinoderm [Dendraster excentricus] fertilization test), and if toxicity was found, further testing was conducted using 3 chronic whole‐effluent toxicity tests. This additional testing included the embryo larval development 72‐h echinoderm (D. excentricus); 7‐d mysid (Americamysis bahia) survival, growth, and fecundity invertebrate test; and 7‐d topsmelt (Atherinops affinis) survival and growth fish test. Toxicity identification evaluations were performed on 3 discharges that consistently elicited a toxic response during whole‐effluent toxicity testing. To place the results of the toxicity testing into the context of environmental risk, the spatial extent of potential biological effects was investigated using the CORMIX mixing zone model. The output of the modeling indicated that discharge of selected effluents did not result in concentrations, or duration of exposure, that would elicit toxic effects to organisms living in the surrounding environment. The present study provides a comprehensive data set that was used to characterize potential toxicity and environmental risk of MODU “miscellaneous discharges” which could help inform future risk assessments of these discharges. Environ Toxicol Chem 2019;38:2811–2823. © 2019 SETAC
Co-Deposition of IgM and C3 May Indicate Unfavorable Renal Outcomes in Adult Patients with Primary Focal Segmental Glomerulosclerosis

Background/Aims: We aimed to investigate the effects of glomerular IgM and C3 deposition on outcomes of adult patients with primary focal segmental glomerulosclerosis (FSGS). Methods: In this retrospective analysis, 86 consecutive adult patients with biopsy-proven primary FSGS were stratified into 3 groups according to their histopathological features: IgM– C3–, IgM+ C3–, and IgM+ C3+. Primary outcome was defined as at least a 50% reduction in baseline estimated glomerular filtration rate (eGFR) or development of kidney failure, while complete or partial remission rates were secondary outcomes. Results: Glomerular IgM deposits were found in 44 (51.1%) patients, 22 (25.5%) of which presented with accompanying C3 deposition. Patients in IgM+ C3+ group had higher level of proteinuria (5.6 g/24 h [3.77–8.5], p = 0.073), higher percentage of segmental glomerulosclerosis (20% [12.3–27.2], p = 0.001), and lower levels of eGFR (69 ± 37.2 mL/min/1.73 m2, p = 0.029) and serum albumin (2.71 ± 0.85 g/dL, p = 0.045) at the time of diagnosis. Despite 86.3% of patients in IgM+ C3+ group (19/22) received immunosuppressive treatment, the primary outcome was more common in patients in the IgM+ C3+ group compared with patients in IgM+ C3– and IgM– C3– groups (11 [50%] vs. 2 [9%] and 11 [26.1%] respectively [p = 0.010]). Complete or partial remission rates were lower in patients in the IgM+ C3+ group (5/22, 22.7%), as well (p = 0.043). Multivariate Cox regression analysis revealed that IgM and C3 co-deposition was an independent risk factor associated with primary outcome (hazard ratio 3.355, 95% CI 1.349–8.344, p = 0.009). Conclusions: Glomerular IgM and C3 co-deposition is a predictor of unfavorable renal outcomes in adult patients with primary FSGS.
Neonatal Consumption of Oligosaccharides Greatly Increases L-Cell Density without Significant Consequence for Adult Eating Behavior

Oligosaccharides (OS) are commonly added to infant formulas, however, their physiological impact, particularly on adult health programming, is poorly described. In adult animals, OS modify microbiota and stimulate colonic fermentation and enteroendocrine cell (EEC) activity. Since neonatal changes in microbiota and/or EEC density could be long-lasting and EEC-derived peptides do regulate short-term food intake, we hypothesized that neonatal OS consumption could modulate early EECs, with possible consequences for adult eating behavior. Suckling rats were supplemented with fructo-oligosaccharides (FOS), beta-galacto-oligosaccharides/inulin (GOS/In) mix, alpha-galacto-oligosaccharides (αGOS) at 3.2 g/kg, or a control solution (CTL) between postnatal day (PND) 5 and 14/15. Pups were either sacrificed at PND14/15 or weaned at PND21 onto standard chow. The effects on both microbiota and EEC were characterized at PND14/15, and eating behavior at adulthood. Very early OS supplementation drastically impacted the intestinal environment, endocrine lineage proliferation/differentiation particularly in the ileum, and the density of GLP-1 cells and production of satiety-related peptides (GLP-1 and PYY) in the neonatal period. However, it failed to induce any significant lasting changes on intestinal microbiota, enteropeptide secretion or eating behavior later in life. Overall, the results did not demonstrate any OS programming effect on satiety peptides secreted by L-cells or on food consumption, an observation which is a reassuring outlook from a human perspective.
Extensive land cover change across Arctic–Boreal Northwestern North America from disturbance and climate forcing

A multitude of disturbance agents, such as wildfires, land use, and climate‐driven expansion of woody shrubs, is transforming the distribution of plant functional types across Arctic–Boreal ecosystems, which has significant implications for interactions and feedbacks between terrestrial ecosystems and climate in the northern high‐latitude. However, because the spatial resolution of existing land cover datasets is too coarse, large‐scale land cover changes in the Arctic–Boreal region (ABR) have been poorly characterized. Here, we use 31 years (1984–2014) of moderate spatial resolution (30 m) satellite imagery over a region spanning 4.7 × 106 km2 in Alaska and northwestern Canada to characterize regional‐scale ABR land cover changes. We find that 13.6 ± 1.3% of the domain has changed, primarily via two major modes of transformation: (a) simultaneous disturbance‐driven decreases in Evergreen Forest area (−14.7 ± 3.0% relative to 1984) and increases in Deciduous Forest area (+14.8 ± 5.2%) in the Boreal biome; and (b) climate‐driven expansion of Herbaceous and Shrub vegetation (+7.4 ± 2.0%) in the Arctic biome. By using time series of 30 m imagery, we characterize dynamics in forest and shrub cover occurring at relatively short spatial scales (hundreds of meters) due to fires, harvest, and climate‐induced growth that are not observable in coarse spatial resolution (e.g., 500 m or greater pixel size) imagery. Wildfires caused most of Evergreen Forest Loss and Evergreen Forest Gain and substantial areas of Deciduous Forest Gain. Extensive shifts in the distribution of plant functional types at multiple spatial scales are consistent with observations of increased atmospheric CO2 seasonality and ecosystem productivity at northern high‐latitudes and signal continental‐scale shifts in the structure and function of northern high‐latitude ecosystems in response to climate change.