Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying confidence accuracy characteristic plots to old/new recognition memory experiments

ABSTRACT Confidence-accuracy characteristic (CAC) plots were developed for use in eyewitness identification experiments, and previous findings show that high confidence indicates high accuracy in all studies of adults with an unbiased lineup. We apply CAC plots to standard old/new recognition memory data by calculating response-based and item-based accuracy, one using false alarms and the other using misses. We use both methods to examine the confidence-accuracy relationship for both correct old responses (hits) and new responses (correct rejections). We reanalysed three sets of published data using these methods and show that the method chosen, as well as the relation of lures to targets, determines the confidence-accuracy relation. Using response-based accuracy for hits, high confidence yields quite high accuracy, and this is generally true with the other methods, especially when lures are unrelated to targets. However, when analyzing correct rejections, the relationship between confidence and accuracy is less pronounced. When lures are semantically related to targets, the various CAC plots show different confidence-accuracy relations. The different methods of calculating CAC plots provide a useful tool in analyzing standard old/new recognition experiments. The results generally accord with unequal-variance signal detection models of recognition memory.
Cotranscriptional R-loop formation by Mfd involves topological partitioning of DNA

Significance R-loop structures pose a threat to genomic integrity because their formation can lead to mutagenesis. Mutagenesis drives antibiotic resistance in bacteria and chemotherapy resistance in human cancers; therefore, it is important to understand how R-loops form. Using a combination of in vitro single-molecule experimentation and in vivo mutagenesis assays, we have shown how Mfd, a bacterial protein known for its role in DNA repair, can interact with RNA polymerase to form R-loops. This interaction generates a topological domain in DNA that is highly prone to R-loop formation. The observed mechanism relies on properties of Mfd that are shared by many other proteins, hinting that this is a potentially universal model for R-loop formation. R-loops are nucleic acid hybrids which form when an RNA invades duplex DNA to pair with its template sequence. Although they are implicated in a growing number of gene regulatory processes, their mechanistic origins remain unclear. We here report real-time observations of cotranscriptional R-loop formation at single-molecule resolution and propose a mechanism for their formation. We show that the bacterial Mfd protein can simultaneously interact with both elongating RNA polymerase and upstream DNA, tethering the two together and partitioning the DNA into distinct supercoiled domains. A highly negatively supercoiled domain forms in between Mfd and RNA polymerase, and compensatory positive supercoiling appears in front of the RNA polymerase and behind Mfd. The nascent RNA invades the negatively supercoiled domain and forms a stable R-loop that can drive mutagenesis. This mechanism theoretically enables any protein that simultaneously binds an actively translocating RNA polymerase and upstream DNA to stimulate R-loop formation.
The association of co-morbid asthma and overweight/obese status with healthcare utilization and caregiver perception of health in children 4–17 years, a NHANES study

Abstract Objective Asthma and obesity are two of the most common chronic childhood illnesses. The purpose of this study was to better understand the relationship between co-morbid asthma and obesity in children aged 4–17 and whether it impacts the caregiver’s perception of health and/or healthcare utilization. Methods This was a secondary analysis of the National Health and Nutrition Examination Surveys (NHANES) datasets from 2007 to 2018. Cumulative logistic regression models were used to analyze the caregiver’s perception of health, received healthcare, and overnight hospital stay as dependent variables. Asthma and weight status were included as covariates, with adjustment for age, income, head of the household’s education, gender, race, and insurance. Results The sample included 15,386 children. When looking at weight status in addition to asthma, compared to caregivers of children with current asthma and normal weight, caregivers of children with current asthma and with obesity are more likely to perceive their children as having worse health (OR = 1.73, 95%CI = [1.30, 2.32], p = 0.0003), and are more likely to have more frequent healthcare utilization but the results did not reach a statistical significance. Conclusions Caregiver’s perception of overall health was worse in caregivers of those with co-morbid obesity/asthma than in caregivers of children with asthma alone. This indicates that caregivers of children with co-morbid asthma and obesity have insight into their children’s condition and may be primed for discussion and counseling in the healthcare setting.
Effects of Exercise Sequence and Velocity Loss Threshold During Resistance Training on Following Endurance and Strength Performance During Concurrent Training.

PURPOSE This study aimed to analyze the response to 4 concurrent training interventions differing in the training sequence and in the velocity loss (VL) threshold during strength training (20% vs 40%) on following endurance and strength performance. METHODS A randomized crossover research design was used. Sixteen trained men performed 4 training interventions consisting of endurance training (ET) followed by resistance training (RT), with 20% and 40% VL, respectively (ET + RT20 and ET + RT40), and RT with 20% and 40% VL, respectively, followed by ET (RT20 + ET and RT40 + ET). The ET consisted of running for 10 minutes at 90% of maximal aerobic velocity. The RT consisted of 3 squat sets with 60% of 1-repetition maximum. A 5-minute rest was given between exercises. The oxygen uptake throughout the ET and repetition velocity during RT were recorded. The blood lactate concentration, vertical jump, and squat velocity were measured at preexercise and after the endurance and strength exercises. RESULTS The RT40 + ET protocol showed an impaired running time along with higher ventilatory equivalents compared with those protocols that performed the ET without previous fatigue. No significant differences were observed in the repetitions per set performed for a given VL threshold, regardless of the exercise sequence. The protocols consisting of 40%VL induced greater reductions in jump height and squat velocity, along with elevated blood lactate concentration. CONCLUSIONS A high VL magnitude (40%VL) induced higher metabolic and mechanical stress, as well as greater residual fatigue, on the following ET performance.
Rôle du Leucine Rich Amelogenin Peptide dans la formation et la minéralisation de l’émail

L'email dentaire est la couche de tissu externe calcifie recouvrant la couronne de la dent; c’est la structure la plus mineralisee du corps humain. L'email est synthetise par l’ameloblaste au cours du developpement de la dent, mais cette population cellulaire degenere et regresse totalement lorsque la dent devient fonctionnelle. L'email mature est donc completement depourvu de cellules et de contenu proteique. L’amelogenine, la principale proteine de l’email a la capacite de s’assembler en structures tres organisees de type nanochaines qui vont guider et reguler les cristaux d’hydroxyapatite de l’email en formation. Le Leucine Rich Amelogenin Peptide (LRAP) est un produit de l'epissage alternatif du gene de l'amelogenine ; c’est un peptide court (56kDa), composee des sequences actives et N- et C-terminales de la proteine d’amelogenine complete. Dans ce travail, nous avons cherche a comprendre le role de LRAP dans l’amelogenese. Nous avons montre 1) que LRAP presentait les memes proprietes d’auto-assemblage que la forme complete d’amelogenine et ses produits de clivage ; 2) que LRAP possedait les meme proprietes de regulation des phosphates de calcium que la proteine complete ; et 3) que la conformation de la forme phosphorylee de LRAP etait modifiee par une augmentation de la concentration de calcium dans le milieu environnant contrairement a la forme dephosphorylee de LRAP. Dans un second temps, nous avons etudie les proprietes de signalisation du peptide et confirme nos resultats de mineralisation sur des modeles de culture de cellules de type ameloblastique LS8 et ALC in vitro et sur un modele de culture de germe de premiere molaire de souris ex vivo. Nous avons montre que la presence des deux formes de LRAP, active la cinetique de differenciation des cellules LS8 et ALC in vitro et favorise la formation de cristaux d’HAP organises et allonges. Dans les germes en culture, la presence de LRAP(+P) dans un milieu mineralisant permet une augmentation de la densite et du volume de mineral forme alors que dans un milieu standard, il favorise la differenciation des germes. LRAP(-P) entraine en revanche, la synthese par les ameloblastes secreteurs de longs et fins cristaux d’HAP bien organises. Ce travail pourrait ouvrir de nouvelles strategies de regeneration des tissus de l'email afin de traiter des alterations de la couche d'email resultant de lesions carieuses a l’aide du LRAP(-P) ou de troubles genetiques comme l’amelogenese imparfaite en utilisant plutot le LRAP(+P).
Social work and telehealth: How Patient Aligned Care Team (PACT) social workers in the Veterans Health Administration responded to COVID-19

ABSTRACT In March 2020, the Veterans Health Administration (VA) responded to pandemic shutdowns with a rapid pivot toward providing services via telehealth. Using data on Veterans who received interventions from social workers between 2019 and 2020 at sites that participated in a national program to increase social work staffing in primary care, we examined changes in frequency and modality of social work encounters that occurred with the onset of the COVID-19 pandemic. We found that primary care social workers maintained a consistent level of engagement, with increases in telephone and video telehealth encounters as in-person visits decreased. Through front-line perspectives, we discuss the practical innovations and policies that enabled those changes in care from VA primary care social workers.
Quantifying Training Demands of a 2-Week In-Season Squash Microcycle.

PURPOSE To quantify the demands of specific on- and off-court sessions, using internal and external training load metrics, in elite squash. METHODS A total of 15 professional squash players (11 males and 4 females) wore a 100-Hz triaxial accelerometer/global positioning system unit and heart rate monitor during on-court "Group," "Feeding," "Ghosting," "Matchplay," and off-court "Conditioning" sessions across a 2-week in-season microcycle. Comparisons of absolute training load (total values) and relative intensity (per minute) were made between sessions for internal (session rating of perceived exertion, differential rating of perceived exertion, TRIMP) and external (Playerload, very high-intensity movements [>3.5 m·s-2]) metrics. RESULTS The Group sessions were the longest (79 [12] min), followed by Feeding (55 [15] min), Matchplay (46 [17] min), Conditioning (37 [9] min), and Ghosting (35 [6] min). Time >90% maximum heart rate was the lowest during Feeding (vs all others P < .05) but other sessions were not different (all P > .05). Relative Playerload during Conditioning (14.3 [3.3] arbitrary unit [a.u.] per min, all P < .05) was higher than Ghosting (7.5 [1.2] a.u./min) and Matchplay (6.9 [1.5] a.u./min), with no difference between these 2 sessions (P ≥ .999). Conditioning produced the highest Playerloads (519 [153] a.u., all P < .001), with the highest on-court Playerloads from Group (450 [94] a.u., all P < .001). The highest session rating of perceived exertion (all P < .001), Edward's TRIMP (all P < .001), and TEAM-TRIMP (all P < .019) occurred during the Group sessions. CONCLUSIONS Squash Matchplay does not systematically produce the highest training intensities and loads. Group sessions provide the highest training loads for many internal and external parameters and, therefore, play a central role within the training process. These findings facilitate planning or adjustment of intensity, volume, and frequency of sessions to achieve desirable physical outcomes.
Opinion on the Use of Animal Models in Nonclinical Safety Assessment: Pros and Cons

Nonclinical evaluation of human safety risks for new chemical entities (NCEs) is primarily conducted in conventional healthy animals (CHAs); however, in certain instances, animal models of diseases (AMDs) can play a critical role in the understanding of human health risks. Animal models of diseases may be especially important when there is a need to understand how disease conditions associated with the intended indication might impact risk assessment of NCEs or when CHAs lack the human-specific target of interest (receptor, etc). Although AMDs have potential benefits over CHAs, they also have limitations. Understanding these limitations and optimizing the AMDs of interest should be done prior to proceeding with studies that will guide development of NCE. The purpose of this manuscript is to provide an overview of the major pros and cons of utilization of AMDs in nonclinical safety assessment.
Sex‐specific alterations in NAD+ metabolism in 3xTg Alzheimer’s disease mouse brain assessed by quantitative targeted LC‐MS

Levels of nicotinamide adenine dinucleotide (NAD+) are known to decline with age and have been associated with impaired mitochondrial function leading to neurodegeneration, a key facet of Alzheimer's disease (AD). NAD+synthesis is sustained via tryptophan‐kynurenine (Trp‐Kyn) pathway as de novo synthesis route, and salvage pathways dependent on the availability of nicotinic acid and nicotinamide. While being currently investigated as a multifactorial disease with a strong metabolic component, AD remains without curative treatment and important sex differences were reported in relation to disease onset and progression. The aim of this study was to reveal the potential deregulation of NAD+metabolism in AD with the direct analysis of NAD+precursors in the mouse brain tissue (wild type (WT) versus triple transgenic (3xTg) AD), using a sex‐balanced design. To this end, we developed a quantitative liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) method, which allowed for the measurement of the full spectrum of NAD+precursors and intermediates in all three pathways. In brain tissue of mice with developed AD symptoms, a decrease in kynurenine (Kyn) versus increase in kynurenic acid (KA) levels were observed in both sexes with a significantly higher increment of KA in males. These alterations in Trp‐Kyn pathway might be a consequence of neuroinflammation and a compensatory production of neuroprotective kynurenic acid. In the NAD+ salvage pathway, significantly lower levels of nicotinamide mononucleotide (NMN) were measured in the AD brain of males and females. Depletion of NMN implies the deregulation of salvage pathway critical for maintaining optimal NAD+ levels and mitochondrial and neuronal function.
Frequent Recurrence of Sinonasal Inverted Papilloma With Carcinoma In Situ in a Multifocal Attachment Pattern: A Case Report and Review of the Literature

Sinonasal inverted papilloma (SIP) is a benign tumor originating from the nasal cavity and paranasal sinuses. Sinonasal inverted papilloma is characterized by local infiltration, high recurrence, and malignant transformation, and its associated dysplasia ranges from mild, moderate, severe, carcinoma in situ (CIS) to invasive squamous cell carcinoma. Sinonasal inverted papilloma with carcinoma in situ (IPwCIS) is the highest degree of dysplasia, which is a stage of malignant transformation of IP. Surgical excision and proper adjuvant therapy can help reduce recurrence rates and suppress further deterioration. In this study, we present a patient with IPwCIS who developed 3 recurrences with a multifocal attachment pattern in less than 18 months. We report the clinical manifestations, development, and treatment process in detail. We also performed a literature review to analyze the characteristics of the disease. Despite comprehensive treatment methods, tumor recurrence and further deterioration of IPwCIS persist.
Prognosis of severe lower respiratory tract infected patients with virus detected: a retrospective observational study

Abstract Objectives To compare the prognosis of severe lower respiratory tract infected patients with virus detected and patients with virus undetected by using metagenomic sequencing technology and a series of traditional serological tests. Methods A total of 51 consecutive lower respiratory tract infected patients were enrolled in this study and samples were obtained to perform metagenomic next-generation sequencing (mNGS) and other traditional tests for virus detection. According to the results, patients were divided into a virus-detected (VD) group and a virus-undetected (VUD) group. Meanwhile, patients’ demographic information, relevant baseline indicators and outcome indicators were also collected. Results There were 27 patients in the VD group and 24 patients in the VUD group. Patients in the VD group had a longer mechanical ventilation (MV) supporting time [528.0 h (216.0, 997.0) vs 235.5 h (119.3, 421.3), p = . 003], a higher tracheotomy rate [(63.0 vs. 29.2%), p = . 016] and red blood cell (RBC) transfusion rate [(66.7 vs. 33.3%), p = . 017] compared to the VUD group. The two groups had no significant difference in mortality rate, hospital length of stay (HLOS) or ICU length of stay (ICULOS). Conclusions Virus detected in patients with severe lower respiratory tract infection (LRTI) was not related to a poorer prognosis, but patients in the VD group did need more clinical resources, such as more MV support and RBC transfusion.
Plasma glycerophospholipid profile, erythrocyte n-3 PUFAs, and metabolic syndrome incidence: a prospective study in Chinese men and women.

BACKGROUND Animal studies have highlighted critical roles of glycerophospholipid (GP) metabolism in various metabolic syndrome (MetS)-related features such as dyslipidemia, obesity, and insulin resistance. However, human prospective studies of associations between circulating GPs and risks of MetS are scarce. OBJECTIVES We aimed to investigate whether GPs are associated with incidence of MetS in a well-established cohort. METHODS A total of 1243 community-dwelling Chinese aged 50-70 y without MetS at baseline and followed up for 6 y were included in current analyses. A total of 145 plasma GPs were quantified by high-throughput targeted lipidomics. MetS was defined using the updated National Cholesterol Education Program Adult Treatment Panel III criteria for Asian Americans. RESULTS After 6 y, 429 participants developed MetS. Eleven GPs, especially those with long-chain polyunsaturated fatty acids (LCPUFAs) or very-long-chain polyunsaturated fatty acids (VLCPUFAs) at the sn-2 position, including 1 phosphatidylcholine (PC) [PC(18:0/22:6)], 9 phosphatidylethanolamines (PEs) [PE(16:0/22:6), PE(18:0/14:0), PE(18:0/18:1), PE(18:0/18:2), PE(18:0/20:3), PE(18:0/22:5), PE(18:0/22:6), PE(18:1/22:6), and PE(18:2/22:6)], and 1 phosphatidylserine (PS) [PS(18:0/18:0)], were positively associated with incident MetS (RRs: 1.16-1.30 per SD change; Bonferroni-corrected P < 0.05). In network analysis, the strongest positive association for MetS incidence was evidenced in a module mainly composed of PEs containing C22:6 and PSs [RR: 1.21; 95% CI: 1.12, 1.31 per SD change; Bonferroni-corrected P < 0.05]. This association was more pronounced in participants with lower erythrocyte total n-3 PUFA concentrations [Bonferroni-corrected Pinter(P value for the interaction)< 0.05]. CONCLUSIONS Elevated plasma concentrations of GPs, especially PEs with LCPUFAs or VLCPUFAs at the sn-2 position, are associated with higher risk of incident MetS. Future studies are merited to confirm our findings.
Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow

Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
Wampenite, C18H16, a new organic mineral from the fossil conifer locality at Wampen, Bavaria, Germany

Wampenite, C 18 H 16 , is a new organic mineral from the fossil wood (conifer) locality at Wampen, Fichtelgebirge, Bavaria, Germany. It is monoclinic, space group P 2 1 / a , with a = 6.7331(19), b = 8.689(3), c = 23.709(7) A, β = 90.118(6)°, V = 1387.0(7) A 3 and Z = 4. Its structure was determined by single-crystal X-ray diffraction, which revealed that the molecular structure comprises an aromatic phenanthrene moiety with an axial methyl group at one end and a disordered propen-2-yl (methylvinyl) terminal group at the other. High resolution mass spectrometry (HRMS) confirmed the molecular formula C 18 H 16 and the IR spectrum is consistent with the molecular structure found.
Formulation of buccal microemulsions containing fluocinolone acetonide

Objectives: The purpose of the present work is to formulate buccal microemulsions (MEs) of fluocinolone acetonide (FA). Methods: Solubilities of FA in different oils were determined for screening of MEs components. In order to determine the concentration ranges of components in MEs, pseudo-ternary phase diagrams were constructed using water titration method. Only the area covered by the transparent region was termed as the ME existence region. The suitable ratio was selected to prepare 0.1% FA ME preparations. Results: Due to high solubility of FA in clove oil (25.22 mg/ml) and peppermint oil (9.5 mg/ml), these two oils were selected to develop ME systems. The pseudo-ternary phase diagram was composed of clove oil or peppermint oil, Tween 80, PEG 400 and water. The phase diagram containing surfactant mixture (S mix ) (2:1) provided a larger ME region than the one containing S mix (1:1). Turbid 0.1% FA MEs were obtained from the blank ME systems containing S mix (1:1) and precipitation of FA was observed in 24 hours . However, clear 0.1 % FA MEs without precipitation were received when prepared in blank MEs of 3.5% clove oil, 31.5% S mix (2:1), 65 % water and 15% peppermint oil, 35% S mix (2:1), 50% water. Conclusion: Pseudo-ternary phase diagrams containing clove oil or peppermint oil were constructed in order to formulate buccal microemulsions of FA. The use of S mix (2:1) ratio of Tween80 to PEG400 provided a larger ME region in phase diagrams compared with S mix (1:1) ratio. In addition, the blank MEs containing S mix (2:1) dissolved FA better than the one containing S mix (1:1) ratio.