Miracle-dz/UniFAR-FTUs huggingface dataset:
Theoretical analysis of the hydrodynamic filtering system in the balaenid whales suspension feeding

Balaenid whales are giant filter feeders that feed on the dense aggregations of prey. Through their unique oral filters, they can effectively filter water out and leave prey in their mouths. In this study, a theoretical model is established to analyze the hydrodynamic filtering system in the balaenid whales suspension feeding. First, the appropriate velocity profiles in the anteroposterior and mediolateral directions are adopted to approximate the flow field in the anteroposterior channel along the tongue (APT channel). Then, a four-stage Runge–Kutta method is used to calculate the particle trajectories and predict the corresponding filter cake profile by solving the particle motion equations. Finally, the effects of three crucial parameters, i.e. the APT channel width D T , the fringe layer permeability K, and the food particle diameter d p, are discussed. The results show that the particle trajectories consist of a series of backward-outward arcs and the food particles tend to accumulate in the posterior region of the oral cavity. The growing parabolic filter cake profiles are formed except for the case of extremely low permeability. A small D T and large K make the tendency of particle posterior aggregation obviously. So squeezing the tongue and having larger fringe layer permeability are both conducive to the swallowing process. But the change in d p has less influence on this tendency. The proposed theoretical analysis method is a fast and low-cost calculation method. The study on the balaenid whales’ filter feeding biomechanics and hydrodynamics is helpful to guide the design of the high-efficiency bionic filters.
Electoral College bias and the 2020 presidential election

Significance Donald Trump's 2016 victory in the Electoral College without leading in the popular vote has led to speculation of a repeat in 2020. If the Democrats were to win the popular vote but by less than a landslide, could they be thwarted from stopping Trump once again? We examine how Electoral College outcomes are conditioned by how states had voted in previous elections. Our simulations suggest that in 2020, the Electoral College bias is likely to again favor the Republicans. However, the expectation is less distortion of the popular will than in 2016. There is even the possibility that if Trump was to win the 2020 popular vote by a slim margin, it could be he who loses the Electoral College. Donald Trump’s 2016 win despite failing to carry the popular vote has raised concern that 2020 would also see a mismatch between the winner of the popular vote and the winner of the Electoral College. This paper shows how to forecast the electoral vote in 2020 taking into account the unknown popular vote and the configuration of state voting in 2016. We note that 2016 was a statistical outlier. The potential Electoral College bias was slimmer in the past and not always favoring the Republican candidate. We show that in past presidential elections, difference among states in their presidential voting is solely a function of the states’ most recent presidential voting (plus new shocks); earlier history does not matter. Based on thousands of simulations, our research suggests that the bias in 2020 probably will favor Trump again but to a lesser degree than in 2016. The range of possible outcomes is sufficiently wide, however, to even include some possibility that Joseph Biden could win in the Electoral College while barely losing the popular vote.
Muscle Typology of World-Class Cyclists across Various Disciplines and Events.

PURPOSE Classical track-and-field studies demonstrated that elite endurance athletes exhibit a slow muscle typology, while elite sprint athletes have a predominant fast muscle typology. In elite cycling, conclusive data on muscle typology are scarce, which may be due to the invasive nature of muscle biopsies. The non-invasive estimation of muscle typology through the measurement of muscle carnosine enabled to explore the muscle typology of 80 world-class cyclists of different disciplines. METHODS The muscle carnosine content of 80 cyclists (4 bicycle motor cross racing (BMX), 33 track, 8 cyclo-cross, 24 road and 11 mountain bike) was measured in the soleus and gastrocnemius by proton magnetic resonance spectroscopy and expressed as a z-score relative to a reference population. Track cyclists were divided into track sprint and endurance cyclists based on their UCI-ranking. Moreover, road cyclists were further characterized based on the percentage of UCI points earned during either single- and multi-stage races. RESULTS BMX cyclists (carnosine aggregate z-score of 1.33) are characterized by a faster muscle typology than track, cyclo-cross, road and mountain bike cyclists (carnosine aggregate z-score of -0.08, -0.76, -0.96 and -1.02, respectively: P<0.05). Track cyclists also possess a faster muscle typology compared to mountain bikers (P=0.033) and road cyclists (P=0.005). Moreover, track sprinters show a significant faster muscle typology (carnosine aggregate z-score of 0.87) compared to track endurance cyclists (carnosine aggregate z-score of -0.44) (P<0.001). In road cyclists, the higher the carnosine aggregate z-score, the higher the percentage of UCI points gained during single-stage races (r=0.517, P=0.010). CONCLUSIONS Prominent differences in the non-invasively determined muscle typology exist between elite cyclists of various disciplines, which opens opportunities for application in talent orientation and transfer.
Ocurrencia de Enteroparásitos en Poblaciones de Quiscalus lugubris (Aves: Passeriformes, Icteridae) del Semiárido Urbano del Estado Falcón, Venezuela

Intestinal parasites in passerine birds can potentially have zoonotic importance. A study was conducted to determine the occurrence of intestinal parasites in feces of Carib Grackle, Quiscalus lugubris, populations (Aves, Passeriformes: Icteridae), in the city of Coro, Falcon State, Venezuela. Parasitological examination of the samples (n=156) was conducted by applying the direct smear, Willis-Molloy (NaCl) and Faust (zinc sulphate) flotation methods, spontaneous sedimentation in tube technique and Kinyoun staining. One or up to three intestinal protozoa, helminths and acanthocephalan taxa were detected in 109 (69.9%) fecal samples. Isospora spp (59.0%), Criptosporidium spp (37.8%) and the spiny-headed worm Mediorhynchus spp (6.4%) were the most frequent enteric parasites. All of the detected parasites are new records for Q. lugubris in Venezuela.
Neonatal Seizures and Purinergic Signalling

Neonatal seizures are one of the most common comorbidities of neonatal encephalopathy, with seizures aggravating acute injury and clinical outcomes. Current treatment can control early life seizures; however, a high level of pharmacoresistance remains among infants, with increasing evidence suggesting current anti-seizure medication potentiating brain damage. This emphasises the need to develop safer therapeutic strategies with a different mechanism of action. The purinergic system, characterised by the use of adenosine triphosphate and its metabolites as signalling molecules, consists of the membrane-bound P1 and P2 purinoreceptors and proteins to modulate extracellular purine nucleotides and nucleoside levels. Targeting this system is proving successful at treating many disorders and diseases of the central nervous system, including epilepsy. Mounting evidence demonstrates that drugs targeting the purinergic system provide both convulsive and anticonvulsive effects. With components of the purinergic signalling system being widely expressed during brain development, emerging evidence suggests that purinergic signalling contributes to neonatal seizures. In this review, we first provide an overview on neonatal seizure pathology and purinergic signalling during brain development. We then describe in detail recent evidence demonstrating a role for purinergic signalling during neonatal seizures and discuss possible purine-based avenues for seizure suppression in neonates.
A representation model for biological entities by fusing structured axioms with unstructured texts

MOTIVATION Structured semantic resources, for example, biological knowledge bases (KBs) and ontologies, formally define biological concepts, entities and their semantic relationships, manifested as structured axioms and unstructured texts (e.g., textual definitions). The resources contain accurate expressions of biological reality and have been used by machine-learning models to assist intelligent applications like knowledge discovery. The current methods use both the axioms and definitions as plain texts in representation learning. However, since the axioms are machine-readable while the natural language is human-understandable, difference in meaning of token and structure impedes the representations to encode desirable biological knowledge. RESULTS We propose ERBK, a representation learning model of bio-entities. Instead of using the axioms and definitions as a textual corpus, our method uses knowledge graph embedding method and deep convolutional neural models to encode the axioms and definitions respectively. The representations could not only encode more underlying biological knowledge but also be further applied to zero-shot circumstance where existing approaches fall short. Experimental evaluations show that ERBK outperforms the existing methods for predicting protein-protein interactions and gene-disease associations. Moreover, it shows that ERBK still maintains promising performance under the zero-shot circumstance. We believe the representations and the method have certain generality and could extend to other types of bio-relation. AVAILABILITY The source code is available at the gitlab repository https://gitlab.com/BioAI/erbk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Custom‐made trays for targeted treatment of oral vesiculobullous diseases: A proposed protocol

Topical and intralesional corticosteroids (CS) are effective treatments for oral manifestations of autoimmune vesiculobullous diseases (VBD); however, may cause unnecessary absorption in the adjacent healthy mucosal surfaces, local infections, atrophy, and injection pain. To propose a protocol using a unique modality for targeted administration of CS for the treatment of local manifestations of oral VBD. The medical records of nine patients with systemic CS‐resistant VBD oral lesions, were reviewed following 3 weeks of treatment and 3 months of tapering using a custom‐made tray designed for precise application of topical CS targeted to the involved mucosa. Following treatment, lesions have healed in 8/9 patients. Involvement of surrounding mucosa was minimal, and no systemic adverse effects were recorded. The proposed protocol using custom‐made trays for targeted CS treatment could be an effective alternative treatment for oral VBD.
Epidemiologic Evaluation and Risk Communication Regarding the Recent Reports of Sudden Death after Influenza Vaccination in the COVID-19 Pandemic

https://jkms.org To prevent the twin-demic, where the COVID-19 pandemic and the 2020-21 influenza epidemic overlap, Korea started a national influenza vaccination program on September 25, 2020. Although the program has been conducted annually, protocol violations during the vaccine transport have been reported this year which led to public anxiety and the Korea Centers for Disease Control and Prevention (KCDC) decided to stop vaccination for 2 weeks.1 During the period, the KCDC reviewed and investigated the quality and safety of the vaccines. Recently, multiple cases of death after vaccination are being reported through mass media, which brought about chaos in the field and public doubts on the safety of vaccination. Distrust in the national vaccine program can cause a fundamental problem in public health, and concerns are growing as it can lead to campaigns against vaccines as in the United States and Europe.
RNA sequencing and Immunohistochemistry Reveal ZFN7 as a Stronger Marker of Survival than Molecular Subtypes in G-CIMP–negative Glioblastoma

Purpose: Glioblastoma is the most aggressive brain tumor in adults and has few therapeutic options. The study of molecular subtype classifications may lead to improved prognostic classification and identification of new therapeutic targets. The Cancer Genome Atlas (TCGA) subtype classification has mainly been applied in U.S. clinical trials, while the intrinsic glioma subtype (IGS) has mainly been applied in European trials. Experimental Design: From paraffin-embedded tumor samples of 432 patients with uniformly treated, newly diagnosed glioblastoma, we built tissue microarrays for IHC analysis and applied RNA sequencing to the best samples to classify them according to TCGA and IGS subtypes. Results: We obtained transcriptomic results from 124 patients. There was a lack of agreement among the three TCGA classificatory algorithms employed, which was not solely attributable to intratumoral heterogeneity. There was overlapping of TCGA mesenchymal subtype with IGS cluster 23 and of TCGA classical subtype with IGS cluster 18. Molecular subtypes were not associated with prognosis, but levels of expression of 13 novel genes were identified as independent prognostic markers in glioma-CpG island methylator phenotype–negative patients, independently of clinical factors and MGMT methylation. These findings were validated in at least one external database. Three of the 13 genes were selected for IHC validation. In particular, high ZNF7 RNA expression and low ZNF7 protein expression were strongly associated with longer survival, independently of molecular subtypes. Conclusions: TCGA and IGS molecular classifications of glioblastoma have no higher prognostic value than individual genes and should be refined before being applied to clinical trials.
Meconium Exposure to Phthalates, Sex and Thyroid Hormones, Birth Size and Pregnancy Outcomes in 251 Mother–Infant Pairs from Shanghai

Phthalates are hormonally active pollutants. In-utero exposure to phthalates has been reported to be associated with birth size parameters and pregnancy outcomes. However, previous reports were inconsistent. We examined the associations between meconium exposure to phthalates and the effects on birth size parameters, pregnancy outcomes and sex and thyroid hormones in 251 mother–infant pairs from a Shanghai hospital. We measured 10 metabolites of phthalates in meconium samples collected during the first 24h after delivery. Information on seven birth size parameters (birth weight, birth length, abdominal circumference, head circumference, femur length, biparietal diameter and anogenital distance) and three pregnancy outcomes (gestational diabetes, premature rupture of membrane, and premature birth) was available from the birth record. Concentrations of free testosterone, estradiol (E2), thyroid stimulating hormone, concentrations of total and free thyroxine and triiodothyronine were measured from cord blood. Multivariate linear regression and logistic regression were used to estimate associations between phthalate exposure and health outcomes. mono-iso-butylphthalate (MiBP), mono-n-butylphthalate (MnBP) and mono-2-ethyl-5-oxohexyl phthalate (MEOHP) were positively associated with birth length and femur length which seemed more obvious in female newborn; MiBP, MnBP and mono-2-ethylhexylphthalate (MEHP) were positively associated with gestational diabetes mellitus (GDM) only in mothers with male newborns; monomethyl phthalate (MMP), MiBP and MEOHP were positively associated with E2 in male newborns. This study indicates that meconium exposure to phthalates may adversely affect some fetal growth parameters and GDM with a potential gender effect.
Descending Control of Limb Movements in Drosophila melanogaster

Descending Control of Limb Movements in Drosophila melanogaster by Cynthia Tien-Cynn Hsu Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Vikas Bhandawat, Supervisor ___________________________ Stephen Lisberger, Chair ___________________________ Marc Sommer ___________________________ Rebecca Yang An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2016
Frequency response areas of neurons in the mouse inferior colliculus. III. Time-domain responses: Constancy, dynamics, and precision in relation to spectral resolution, and perception in the time domain

The auditory midbrain (central nucleus of inferior colliculus, ICC) receives multiple brainstem projections and recodes auditory information for perception in higher centers. Many neural response characteristics are represented in gradients (maps) in the three-dimensional ICC space. Map overlap suggests that neurons, depending on their ICC location, encode information in several domains simultaneously by different aspects of their responses. Thus, interdependence of coding, e.g. in spectral and temporal domains, seems to be a general ICC principle. Studies on covariation of response properties and possible impact on sound perception are, however, rare. Here, we evaluated tone-evoked single neuron activity from the mouse ICC and compared shapes of excitatory frequency-response areas (including strength and shape of inhibition within and around the excitatory area; classes I, II, III) with types of temporal response patterns and first-spike response latencies. Analyses showed covariation of sharpness of frequency tuning with constancy and precision of responding to tone onsets. Highest precision (first-spike latency jitter < 1 ms) and stable phasic responses throughout frequency-response areas were the quality mainly of class III neurons with broad frequency tuning, least influenced by inhibition. Class II neurons with narrow frequency tuning and dominating inhibitory influence were unsuitable for time domain coding with high precision. The ICC center seems specialized rather for high spectral resolution (class II presence), lateral parts for constantly precise responding to sound onsets (class III presence). Further, the variation of tone-response latencies in the frequency-response areas of individual neurons with phasic, tonic, phasic-tonic, or pauser responses gave rise to the definition of a core area, which represented a time window of about 20 ms from tone onset for tone-onset responding of the whole ICC. This time window corresponds to the roughly 20 ms shortest time interval that was found critical in several auditory perceptual tasks in humans and mice.
Institution-Specific Machine Learning Models for Prehospital Assessment to Predict Hospital Admission: Prediction Model Development Study

Background Although multiple prediction models have been developed to predict hospital admission to emergency departments (EDs) to address overcrowding and patient safety, only a few studies have examined prediction models for prehospital use. Development of institution-specific prediction models is feasible in this age of data science, provided that predictor-related information is readily collectable. Objective We aimed to develop a hospital admission prediction model based on patient information that is commonly available during ambulance transport before hospitalization. Methods Patients transported by ambulance to our ED from April 2018 through March 2019 were enrolled. Candidate predictors were age, sex, chief complaint, vital signs, and patient medical history, all of which were recorded by emergency medical teams during ambulance transport. Patients were divided into two cohorts for derivation (3601/5145, 70.0%) and validation (1544/5145, 30.0%). For statistical models, logistic regression, logistic lasso, random forest, and gradient boosting machine were used. Prediction models were developed in the derivation cohort. Model performance was assessed by area under the receiver operating characteristic curve (AUROC) and association measures in the validation cohort. Results Of 5145 patients transported by ambulance, including deaths in the ED and hospital transfers, 2699 (52.5%) required hospital admission. Prediction performance was higher with the addition of predictive factors, attaining the best performance with an AUROC of 0.818 (95% CI 0.792-0.839) with a machine learning model and predictive factors of age, sex, chief complaint, and vital signs. Sensitivity and specificity of this model were 0.744 (95% CI 0.716-0.773) and 0.745 (95% CI 0.709-0.776), respectively. Conclusions For patients transferred to EDs, we developed a well-performing hospital admission prediction model based on routinely collected prehospital information including chief complaints.
Choriocapillaris Vascular Parameters in Normal Eyes and Those with Pachychoroid with and without Disease.

PURPOSE To evaluate the vascular characteristics of the choriocapillaris in eyes with pachychoroid as compared with normal controls. METHODS Eyes with pachychoroid disease were defined as those with a history of central serous chorioretinopathy or peripapillary pachychoroid syndrome. Pachychoroid without disease was defined as eyes with no history of disease with a subfoveal choroidal thickness ≥ the age-adjusted 95 percentile thickness. Frame averaged optical coherence tomography angiography images of the choriocapillaris obtained with a Zeiss Plex Elite were binarized, skeletonized, and evaluated for vascular branching parameters. RESULTS There were 7 normal controls, 10 pachychoroid without disease, and 17 pachychoroid disease subjects. Mean choriocapillaris vessel segment length was 12.19 µm in eyes with pachychoroid disease as compared with 11.48 µm for normal controls and 11.62 µm for pachychoroid without disease (P=.003 and P=.006, respectively). The branches per mm were fewer in pachychoroid disease, 1215, as compared to normal controls, 1471, or pachychoroid without disease, 1384, (P<.001, and P = .002, respectively). The choriocapillaris vessel diameter was larger, but the fractal dimension was smaller in pachychoroid disease eyes as compared to normal or pachychoroid without disease eyes. There was no statistically significant difference between normal controls and pachychoroid without disease for any measured vascular parameter of the choriocapillaris. CONCLUSIONS Choriocapillaris vascular parameters suggest that pachychoroid is not necessarily pathologic. It is possible choroidal thickening is an epiphenomenon and there are more significant vascular parameters that are related to disease. These concepts may help guide future prospective studies.