Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Contamination Patterns of Listeria monocytogenes in Flammulina velutipes Plants

Abstract Four mushroom (Flammulina velutipes) production plants were sampled to investigate the prevalence and contamination source of Listeria monocytogenes. Among 295 samples, the prevalence of L. monocytogenes was 18.6%; the contamination appeared to originate from the mycelium-scraping machinery, contaminating both the product and upstream packaging equipment. Of 55 L. monocytogenes isolates, lineages I.1 (1/2a-3a) and II.2 (1/2b-3b-7) accounted for 65.5% and 34.5%, respectively. In addition, lineage I.1 formed significantly thicker biofilms than those within lineage II.2, as determined by crystal violet staining and scanning electron microscopy. Genotype analyses of L. monocytogenes isolates using enterobacteria repetitive intergenic consensus-polymerase chain reaction, and random amplified polymorphic DNA revealed that the surfaces of mycelium-scraping machinery may serve as the main source of L. monocytogenes contamination in three of the four plants. This study was the first report to explore the .
A CMV-induced adaptive human Vδ1+ γδ T cell clone recognizes HLA-DR

Deseke et al. use soluble γδ TCRs and CRISPR/Cas9-mediated screening to identify the MHC class II surface receptor HLA-DR as the cognate TCR ligand of a CMV-induced Vδ1+ γδ T cell clone, which is cross-recognizing leukemia cells.
Performance of Early Capillary Refill Time Measurement on Outcomes in Cardiogenic Shock: An Observational, Prospective Multicentric Study.

BACKGROUND Identification of cardiogenic shock severity is a critical step to adapt the management level upon admission. Peripheral tissue perfusion signs, simple and reliable markers of tissue hypoperfusion have never been extensively assessed during cardiogenic shock. METHODS All consecutive patients admitted in ICU for cardiogenic shock of two tertiary teaching hospitals were included in a prospective observational study. Macro-hemodynamic parameters (such as heart rate, blood pressure, left ventricular ejection fraction and cardiac index) and peripheral tissue perfusion signs such as capillary refill time on the index fingertip, mottling and Pv-aCO2 (the difference between partial pressure of CO2 in venous blood and arterial blood) were recorded at inclusion (H0), H6, H12, H24 and H48. The composite primary endpoint was the association between 90-day mortality or the need for venoarterial-ECMO support. RESULTS 61 patients were included; at inclusion, simplified acute physiology score II was 64 (52-77) points. The primary endpoint was met by 42% of patients. Capillary refill time values were significantly higher at all time-points in non survivors or patients needing venoarterial-ECMO support. In univariate analysis, capillary refill time > 3 sec at inclusion was associated with 90-day all-cause mortality or venoarterial-ECMO support (Hazard Ratio of 12.38; 95% CI 2.91 to 52.71). Capillary refill time at inclusion was poorly associated with macrocirculatory parameters but significantly correlated with microcirculatory parameters. Further, capillary refill time added incremental value to Cardshock score, with an AUC combination at 0.93. CONCLUSION In patients admitted in ICU for cardiogenic shock, our preliminary data suggest that a prolonged capillary refill time > 3 sec was associated with an early prediction of 90-day mortality or the need for venoarterial-ECMO support. Clinical trial registration available at www. CLINICALTRIALS gov, ID: NCT0343664.
Is it all in the Family? Sexual Identity Differences in Dsm-5 Alcohol and Other Drug Use Disorders and Associations with Alcohol and Other Drug Misuse History among Parents, Offspring, and Other Relatives

Background: The objectives of this study were to: (1) estimate the prevalence of family history of alcohol and other drug (AOD) misuse (positive family history [FH+]) in first- and second-degree relatives across sexual identity subgroups (i.e., lesbian, gay, bisexual, heterosexual); (2) compare AOD misuse among offspring of sexual minority and heterosexual parents; and (3) examine the relationships between FH+ and the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) alcohol use disorder (AUD) and other drug use disorder (ODUD) across sexual identity subgroups. Methods: Data were from the National Epidemiologic Survey on Alcohol and Related Conditions-III (n = 36,309 non-institutionalized U.S. adults aged ≥ 18 years). Data collection occurred in households using structured diagnostic face-to-face interviews during 2012–2013. Results: The presence of FH+ in first- and second-degree relatives was most prevalent among bisexual women relative to all other sexual orientation subgroups. Multivariable regression analyses indicated that the odds of AUD and ODUD were higher among FH+ adults relative to negative family history (FH-) adults. Lesbian and bisexual women had higher odds of AUD compared to heterosexual women, controlling for any FH+; this sexual identity difference was not found for men. There were no significant differences in ODUD between heterosexual FH- men and gay FH- men. We found differences in AOD misuse among offspring of bisexual parents, but not gay or lesbian parents compared to heterosexual parents. Conclusions: Health professionals should consider the higher likelihood of a family history of AOD misuse among sexual minorities, especially bisexual women, when treating these individuals. The lack of differences in AOD misuse among offspring of gay or lesbian parents relative to heterosexual parents warrants attention for legal, policy, and clinical decisions.
Comparing Racial Differences in Emphysema Prevalence Among Adults With Normal Spirometry: A Secondary Data Analysis of the CARDIA Lung Study

BACKGROUND Computed tomography (CT) imaging complements spirometry and may provide insight into racial disparities in respiratory health. OBJECTIVE To determine the difference in emphysema prevalence between Black and White adults with different measures of normal spirometry results. DESIGN Observational study using clinical data and spirometry from the CARDIA (Coronary Artery Risk Development in Young Adults) study obtained in 2015 to 2016 and CT scans done in 2010 to 2011. SETTING 4 U.S. centers. PARTICIPANTS Population-based sample of Black and White adults. MEASUREMENTS Self-identified race and visually identified emphysema on CT in participants with different measures of "normal" spirometry results, calculated using standard race-specific and race-neutral reference equations. RESULTS A total of 2674 participants (485 Black men, 762 Black women, 659 White men, and 768 White women) had both a CT scan and spirometry available for analysis. Among participants with a race-specific FEV1 between 80% and 99% of predicted, 6.5% had emphysema. In this group, emphysema prevalence was 3.9-fold (95% CI, 2.1- to 7.1-fold; 15.5% vs. 4.0%) higher among Black men than White men and 1.9-fold (CI, 1.0- to 3.8-fold; 6.6% vs. 3.4%) higher among Black women than White women. Among participants with a race-specific FEV1 between 100% and 120% of predicted, 4.0% had emphysema. In this category, Black men had a 6.4-fold (CI, 2.2- to 18.7-fold; 13.9% vs. 2.2%) higher prevalence of emphysema than White men, whereas Black and White women had a similar prevalence of emphysema (2.6% and 2.0%, respectively). The use of race-neutral equations to identify participants with an FEV1 percent predicted between 80% and 120% attenuated racial differences in emphysema prevalence among men and eliminated racial differences among women. LIMITATION No CT scans were obtained during the most recent study visit (2015 to 2016) when spirometry was done. CONCLUSION Emphysema is often present before spirometry findings become abnormal, particularly among Black men. Reliance on spirometry alone to differentiate lung health from lung disease may result in the underrecognition of impaired respiratory health and exacerbate racial disparities. PRIMARY FUNDING SOURCE National Institutes of Health.
LSTformer: Long Short-Term Transformer for Real Time Respiratory Prediction

Since the tumor moves with the patient's breathing movement in clinical surgery, the real-time prediction of respiratory movement is required to improve the efficacy of radiotherapy. Some RNN-based respiratory management methods have been proposed for this purpose. However, these existing RNN-based methods often suffer from the degradation of generalization performance for a long-term window (such as 600 ms) because of the structural consistency constraints. In this paper, we propose an innovative Long Short-term Transformer (LSTformer) for long-term real-time accurate respiratory prediction. Specifically, a novel Long-term Information Enhancement module (LIE) is proposed to solve the performance degradation under a long window by increasing the long-term memory of latent variables. A lightweight Transformer Encoder (LTE) is proposed to satisfy the real-time requirement via simplifying the architecture and limiting the number of layers. In addition, we propose an application-oriented data augmentation strategy to generalize our LSTformer to practical application scenarios, especially robotic radiotherapy. Extensive experiments on our augmented dataset and publicly available dataset demonstrate the state-of-the-art performance of our method on the premise of satisfying the real-time demand.
The pH sensor and ion binding of NhaD Na+/H+ antiporter from IT superfamily

Sodium‐proton (Na+/H+) antiporters from the ion transporter (IT) superfamily play a vital role in controlling the pH and electrolyte homeostasis. However, very limited information regarding their structural functions is available to date. In this study, the structural model of the NhaD antiporter was proposed as a typical hairpin structure of IT proteins, with two symmetrically conserved scaffold domains that frame the core substrate‐binding sites, and four motifs were identified. Furthermore, 25 conserved sites involving these domains were subjected to site‐directed mutagenesis, and all mutations resulted in an impact on transport abilities. In particular, as candidates for Na+‐binding sites, D166 and D405 mutations at hairpin discontinuities were detrimental to transport activities and were found to induce pronounced conformational changes using fluorescence resonance energy transfer (FRET) assays. In addition, as observed in the NhaA structure, some charged residues, for example, E64, E65, R454, and R464, are predicted to be involved in the net charge switch of NhaD activation, by collectively form a “pH sensor” at the entrance of the cytoplasmic funnel. Mutations encompassing these residues were detrimental to the transport activity of NhaD or lost the capacity to respond to pH signals and trigger conformational changes for Na+ translocation.
Attachment Security Priming Affecting Mating Strategies Endorsement among College Students

Exposure to environmental cues reflecting potential threats to future survivability is associated with a stronger endorsement of short-term mating strategies. Less is known, however, about the effects of safety and security cues. In four studies, we examined the effects of attachment-related security cues compared to neutral cues on preferences for short- and long-term mating strategies. Preferences were assessed using self-report and behavioral measures. In line with Life History Theory (LHT) and our hypotheses, exposure to attachment-related security cues was mainly associated with a stronger preference for long-term mating strategies and a weaker preference for short-term strategies. Our internal meta-analysis of the experimental security manipulations across studies provided further support for the association between state attachment security and endorsement of mating strategies. We also found some predictable effects of gender and relationship status. Implications for LHT and attachment theory are discussed. (139 words)
Administrative codes may have limited utility in diagnosing biliary colic in emergency department visits: A validation study

Backgrounds/Aims Biliary colic is a common cause of emergency department (ED) visits; however, the natural history of the disease and thus the indications for urgent or scheduled surgery remain unclear. Limitations of previous attempts to elucidate this natural history at a population level are based on the reliance on the identification of biliary colic via administrative codes in isolation. The purpose of our study was to validate the use of International Statistical Classification of Diseases and Related Health Problems codes, 10th Revision, Canadian modification (ICD-10-CA) from ED visits in adequately differentiating patients with biliary colic from those with other biliary diagnoses such as cholecystitis or common bile duct stones. Methods We performed a retrospective validation study using administrative data from two large academic hospitals in Toronto. We assessed all the patients presenting to the ED between January 1, 2012 and December 31, 2018, assigned ICD-10-CA codes in keeping with uncomplicated biliary colic. The codes were compared to the individually abstracted charts to assess diagnostic agreement. Results Among the 991 patient charts abstracted, 26.5% were misclassified, corresponding to a positive predictive value of 73% (95% confidence interval 73%–74%). The most frequent reasons for inaccurate diagnoses were a lack of gallstones (49.8%) and acute cholecystitis (27.8%). Conclusions Our findings suggest that the use of ICD-10 codes as the sole means of identifying biliary colic to the exclusion of other biliary pathologies is prone to moderate inaccuracy. Previous investigations of biliary colic utilizing administrative codes for diagnosis may therefore be prone to unforeseen bias.
Risk factors in distal interphalangeal joint arthrodesis in the hand: a retrospective study of 173 cases

In this retrospective study we aimed to analyse the risk factors for complications after different methods of distal interphalangeal arthrodesis in the hand. Forty-four per cent were treated with K-wire/cerclage fixation, 46% with X-fuse® implants (Stryker GmbH, Selzach, Switzerland) and 10% with headless compression screws (HBS®-screw, KLS Martin Group, Tuttlingen, Germany). The median follow-up was 16 weeks (range 6–224). The overall complication incidence was 44% (minor complications 29% and major 15%). The logistic regression showed that osteoarthritis, revisional arthrodesis and smoking had a negative impact on the total complication incidence. A Cox-regression analysis showed that HBS®-screw arthrodesis was associated with a significantly lower incidence of major complications compared with K-wire/cerclage and X-Fuse®-arthrodesis. Revisional arthrodesis was five times more frequently connected with major complications than primary surgery. Smokers were three times more likely to experience major complications than non-smokers. We conclude that arthrodesis of the distal interphalangeal joint often leads to complications. Risk factors must be kept in mind. Level of evidence: III
Who Wants to Shop With You: Joint Product–Participant Recommendation for Group-Buying Service

Recent years have witnessed the great success of group buying (GB) in social e-commerce, opening up a new way of online shopping. In this business model, a user can launch a GB as an initiator to share her interested product with social friends. The GB is clinched once enough friends join in as participants to copurchase the shared product. As such, a successful GB depends on not only whether the initiator can find her interested product but also whether the friends are willing to join in as participants. Most existing recommenders are incompetent in such complex scenario, as they merely seek to help users find their preferred products and cannot help identify potential participants to join in a GB. To this end, we propose a novel joint product–participant recommendation (J2PRec) framework, which recommends both candidate products and participants for maximizing the success rate of a GB. Specifically, J2PRec first designs a relational graph embedding module, which effectively encodes the various relations in GB for learning enhanced user and product embeddings. It then jointly learns the product and participant recommendation tasks under a probabilistic framework to maximize the GB likelihood, i.e., boost the success rate of a GB. Extensive experiments on three real-world datasets demonstrate the superiority of J2PRec for GB recommendation.
Torque Calculation of Five-Phase Interior Permanent Magnet Machine Using Improved Analytical Method

This paper proposes a new torque analytical method (AM) for five-phase interior permanent magnet synchronous machine (IPMSM) with shifted asymmetrical rotor pole. The key of this method is to consider the permanent magnet (PM) torque and the reluctance torque simultaneously, by using the Lorenz force law. The analytical expressions, including stator magnetomotive force (MMF), rotor MMF generated by PMs and rotor MMF generated by stator MMF, are first derived. Then, Lorentz force law is used to calculate PM torque and reluctance torque, respectively. In order to improve the precision of electromagnetic torque calculation, stator slotting effect under shifted asymmetrical rotor pole is taken into consideration. Finally, the AM is verified by finite element method and experiment. The results show that proposed AM is good enough to predict the torque performance of IPMSM with shifted asymmetrical rotor pole.
Deep Learning to Predict Neonatal and Infant Brain Age from Myelination on Brain MRI Scans.

Background Assessment of appropriate brain myelination on T1- and T2-weighted MRI scans is based on gestationally corrected age (GCA) and requires subjective visual inspection of the brain with knowledge of normal myelination milestones. Purpose To develop a convolutional neural network (CNN) capable of estimating neonatal and infant GCA based on brain myelination on MRI scans. Materials and methods In this retrospective study from one academic medical center, brain MRI scans of patients aged 0-25 months with reported normal myelination were consecutively collected between January 1995 and June 2019. The GCA at MRI was manually calculated. After exclusion criteria were applied, T1- and T2-weighted MRI scans were preprocessed with skull stripping, linear registration, z scoring for normalization, and downsampling. A three-dimensional regression CNN was trained to predict GCA using mean absolute error (MAE) as its loss function. Attention maps were calculated using layer-wise relevance propagation. Models were validated on an external test set from the National Institutes of Health (NIH). Model MAEs were compared using Kruskal-Wallis and Mann-Whitney tests. Results A total of 518 neonates and infants (mean GCA, 67 weeks ± 33 [SD], 56% male) was included, comprising 469 T1-, 438 T2-, and 389 T1- and T2-weighted studies. Across 10 runs, MAEs of T1-, T2-, and T1- and T2-weighted networks were 9.8 ± 2.3, 9.1 ± 1.9, and 7.7 ± 1.7 weeks, respectively. Attention map analysis demonstrated increased network attention to the cerebellum, osterior white matter, and basal ganglia signal in neonates with GCA of less than 40 weeks and the anterior white matter signal in infants with GCA of more than 120 weeks, corresponding to the known progression of myelination. The T1- and T2-weighted network tested on the external NIH test set had an MAE of 9.1 weeks, which was reduced to 5.9 weeks with further training using half the external test set (P < .001). Conclusion A three-dimensional convolutional neural network can predict the gestationally corrected age of neonates and infants aged 0-25 months based on brain myelination patterns on T1- and T2-weighted MRI scans. © RSNA, 2022 Online supplemental material is available for this article.
Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons

Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles. ABSTRACT Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.
A hierarchical anatomical framework and workflow for organizing stereotactic encephalography in epilepsy

Stereotactic electroencephalography (SEEG) is an increasingly utilized method for invasive monitoring in patients with medically intractable epilepsy. Yet, the lack of standardization for labeling electrodes hinders communication among clinicians. A rational clustering of contacts based on anatomy rather than arbitrary physical leads may help clinical neurophysiologists interpret seizure networks. We identified SEEG electrodes on post‐implant CTs and registered them to preoperative MRIs segmented according to an anatomical atlas. Individual contacts were automatically assigned to anatomical areas independent of lead. These contacts were then organized using a hierarchical anatomical schema for display and interpretation. Bipolar‐referenced signal cross‐correlations were used to compare the similarity of grouped signals within a conventional montage versus this anatomical montage. As a result, we developed a hierarchical organization for SEEG contacts using well‐accepted, free software that is based solely on their post‐implant anatomical location. When applied to three example SEEG cases for epilepsy, clusters of contacts that were anatomically related collapsed into standardized groups. Qualitatively, seizure events organized using this framework were better visually clustered compared to conventional schemes. Quantitatively, signals grouped by anatomical region were more similar to each other than electrode‐based groups as measured by Pearson correlation. Further, we uploaded visualizations of SEEG reconstructions into the electronic medical record, rendering them durably useful given the interpretable electrode labels. In conclusion, we demonstrate a standardized, anatomically grounded approach to the organization of SEEG neuroimaging and electrophysiology data that may enable improved communication among and across surgical epilepsy teams and promote a clearer view of individual seizure networks.