Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational errors of the induced electric field in voxelized and tetrahedral anatomical head models exposed to spatially uniform and localized magnetic fields

At low and intermediate frequencies, the strength of the induced electric field is used as dosimetric quantity for human protection in the International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines. To compute the induced electric field, numerical methods based on anatomically realistic voxel models are commonly used. However, grid-based models introduce staircase approximation errors when curved surfaces are discretized with voxels, particularly in correspondence of boundaries with large differences in electrical conductivity. By contrast, those kind of artefacts are absent in tetrahedral meshes. Here, we investigate the computational errors that affect voxelized and tetrahedral head models when exposed to uniform magnetic fields at 50 Hz, and localized exposure due to transcranial magnetic stimulation. Five subjects were considered, and for each of them four voxel grids and four tetrahedral meshes were reconstructed with different resolutions. The differences in the results were characterized by comparing the induced electric fields computed using those meshes/grids. The results showed modest discrepancies in the overall electric field distributions between the various grids and meshes. However, the peak electric field strengths were erroneous for both tetrahedral and voxel models. Therefore, post-processing techniques are needed to suppress those numerical artefacts. For this purpose, the 99.99th, or lower, percentile of the electric field strength was found to remove the numerical errors. In addition, we found that spatially averaging the electric fields over 2 mm cubical volumes, as described by the ICNIRP, was effective in removing most of the spuriously large electric fields. When spatial averaging was used, relative coarse head models consisting of approximately 1 mm voxels or tetrahedral meshes with 2 mm average side length were sufficient to mitigate the artefacts. Nonetheless, the additional percentile filtering might still be needed to suppress the erroneous values completely.
Serotype distribution and antimicrobial resistance of human Salmonella enterica in Bangui, Central African Republic, from 2004 to 2013

Background Limited epidemiological and antimicrobial resistance data are available on Salmonella enterica from sub-Saharan Africa. We determine the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to third-generation cephalosporin (C3G). Methodology/Principal findings A total of 582 non-duplicate human clinical isolates were collected. The most common serotype was Typhimurium (n = 180, 31% of the isolates). A randomly selected subset of S. Typhimurium isolates were subtyped by clustered regularly interspaced short palindromic repeat polymorphism (CRISPOL) typing. All but one invasive isolate tested (66/68, 96%) were associated with sequence type 313. Overall, the rates of resistance were high to traditional first-line drugs (18–40%) but low to many other antimicrobials, including fluoroquinolones (one resistant isolate) and C3G (only one ESBL-producing isolate). The extended-spectrum beta-lactamase (ESBL)-producing isolate and three additional ESBL isolates from West Africa were studied by whole genome sequencing. The blaCTX-M-15 gene and the majority of antimicrobial resistance genes found in the ESBL isolate were present in a large conjugative IncHI2 plasmid highly similar (> 99% nucleotide identity) to ESBL-carrying plasmids found in Kenya (S. Typhimurium ST313) and also in West Africa (serotypes Grumpensis, Havana, Telelkebir and Typhimurium). Conclusions/Significance Although the prevalence of ESBL-producing Salmonella isolates was low in CAR, we found that a single IncHI2 plasmid-carrying blaCTX-M-15 was widespread among Salmonella serotypes from sub-Saharan Africa, which is of concern.
#SafeSport: safeguarding initiatives at the Youth Olympic Games 2018

Background Little is known about athletes’ understanding of safe sport and occurrence of harassment and abuse in elite youth sport. Objective To evaluate the IOC Safe Sport educational experience at the Youth Olympic Games 2018 in Buenos Aires and to ascertain the athletes’ (1) understanding of what constitutes harassment and abuse, (2) perception of the occurrence in their sport, and (3) knowledge of where to report. Methods Athletes visiting the IOC Safe Sport Booth answered a survey related to athletes’ (1) understanding of harassment and abuse in sport, (2) perception of the occurrence of harassment and abuse in their sport, and (3) knowledge of where to report. Experts and volunteers answered an email survey on their experience. Results The response rate was 71.8%. When asked to define ‘safe sport’, the athletes mainly relate the concept to general physical and environmental safety, fair play and clean sport, rather than sport free from harassment and abuse. Almost half (46%) of the athletes expressed surprise by the definition of behaviours of harassment and abuse within sport. When asked if harassment and/or abuse occur in their sport, 47.5% reported ‘no’ or ‘not likely’, while 34% stated ‘likely’ or ‘very likely’; 19% were ‘unsure’. The majority (63%) of athletes knew where to seek help. Three quarters (71%) of the athletes rated the educational materials as ‘good’ to ‘excellent’. The experts and volunteers believed the intervention would result in change in athletes’ awareness, knowledge and behaviour. Conclusions This multinational cohort of elite youth athletes is not knowledgeable of the concept of harassment and abuse in sport, despite there being a significant perception of occurrence of harassment and abuse in their sports.
Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks*

Interactome studies are necessary to understand cellular processes and co-elution methods are well suited for the simultaneous and global exploration of the interactome, as well as the assessment of biological perturbations of the network. These methods rely on the fundamental idea that proteins from the same complex migrate together during fractionation. We review the different separation techniques along with the quantification and bioinformatic approaches used for co-elution methods and provide design considerations to choose between them. Graphical Abstract Highlights Co-elution stands out as a global interactome mapping method. Benefits include all-to-all protein analysis and measurement of interactome perturbations. Different separation, quantification and bioinformatic strategies are available. Design considerations depend largely on system under study. Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into several fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantification and bioinformatic strategies used in co-elution studies, and the important considerations in designing these studies. The benefits of co-elution versus other methods makes it a valuable starting point when asking questions that involve the perturbation of the interactome.
Insular Risk Processing Predicts Alcohol Use Via Externalizing Pathway in Male Adolescents.

OBJECTIVE Male adolescents exhibit greater impulsivity and externalizing symptomatology relative to female adolescents. Furthermore, externalizing symptomatology has been associated with greater alcohol use and differential anterior insula functioning. The current longitudinal study on adolescents examined whether activity in the anterior insula, when processing uncertain outcomes and representing risk, is directly associated with gender differences in later adolescent alcohol use frequency, as well as indirectly through externalizing symptomatology. METHOD Using functional magnetic resonance imaging, we examined whether gender moderated these associations in a sample of 161 adolescents (53% male) with repeated annual measurements over 3 years. We monitored responding of a region implicated in risk processing during an economic lottery choice task involving uncertain outcomes. Self-reported externalizing symptomatology and alcohol use frequency were collected at all time points. RESULTS Results indicated that there was a significant indirect effect of anterior insula processing during the task at Time 1 on alcohol use at Time 3 through externalizing symptomatology at Time 2 for male, but not female, adolescents. Externalizing symptomatology predicted alcohol use for both male and female adolescents. CONCLUSIONS The findings suggest gender differences in vulnerability to later alcohol use, specifically in terms of how a neurobiological susceptibility to risk insensitivity may disproportionately influence male adolescents' externalizing symptomatology. Male adolescents who do not effectively integrate risk-related signals are likely to engage in externalizing behaviors, which in turn are related to later alcohol use. Findings also suggest differential roles of risk-related brain function that contribute to gendered pathways to adolescent health-risk behaviors.
Morphological Assessment of MACI Grafts in Patients with Revision Surgery and Total Joint Arthroplasty

Objective To compare the histological and immunohistochemical characteristics of matrix-assisted chondrocyte implantation (MACI) grafts between patients with revision surgery and patients with total joint arthroplasty. Methods Biopsies of MACI grafts from patients with revision and total joint arthroplasty. The graft tissue characteristics and subchondral bone were examined by qualitative histology, ICRS (International Cartilage Repair Society) II scoring and semiquantitative immunohistochemistry using antibodies specific to type I and type II collagen. Results A total of 31 biopsies were available, 10 undergoing total knee arthroplasty (TKA) and 21 patients undergoing revision surgery. Patients in the clinically failed group were significantly older (46.3 years) than patients in the revision group (36.6 years) (P = 0.007). Histologically, the predominant tissue in both groups was of fibrocartilaginous nature, although a higher percentage of specimens in the revision group contained a hyaline-like repair tissue. The percentages of type I collagen (52.9% and 61.0%) and type II collagen (66.3% and 42.2%) were not significantly different between clinically failed and revised MACI, respectively. The talar dome contained the best and patella the worst repair tissue. Subchondral bone pathology was present in all clinically failed patients and consisted of bone marrow lesions, including edema, necrosis and fibrosis, intralesional osteophyte formation, subchondral bone plate elevation, intralesional osteophyte formation, subchondral bone cyst formation, or combinations thereof. Conclusions MACI grafts in patients with revision and total joint arthroplasty were predominantly fibrocartilage in repair type, did not differ in composition and were histologically dissimilar to healthy cartilage. Clinically failed cases showed evidence of osteochondral unit failure, rather than merely cartilage repair tissue failure. The role of the subchondral bone in relation to pain and failure and the pathogenesis warrants further investigation.
The µMCTQ: An Ultra-Short Version of the Munich ChronoType Questionnaire

Individuals vary in how their circadian system synchronizes with the cyclic environment (zeitgeber). Assessing these differences in “phase of entrainment”—often referred to as chronotype—is an important procedure in laboratory experiments and epidemiological studies but is also increasingly applied in circadian medicine, both in diagnosis and therapy. While biochemical measurements (e.g., dim-light melatonin onset [DLMO]) of internal time are still the gold standard, they are laborious, expensive, and mostly rely on special conditions (e.g., dim light). Chronotype estimation in the form of questionnaires is useful in approximating the timing of an individual’s circadian clock. They are simple, inexpensive, and location independent (e.g., administrable on- and offline) and can therefore be easily administered to many individuals. The Munich ChronoType Questionnaire (MCTQ) is an established instrument to assess chronotype by asking subjects about their sleep-wake-behavior. Here we present a shortened version of the MCTQ, the µMCTQ, for use in situations in which instrument length is critical, such as in large cohort studies. The µMCTQ contains only the core chronotype module of the standard MCTQ (stdMCTQ), which was shortened and adapted from 17 to 6 essential questions, allowing for a quick assessment of chronotype and other related parameters such as social jetlag and sleep duration. µMCTQ results correspond well to the ones collected by the stdMCTQ and are externally validated by actimetry and DLMO, assessed at home (no measure of compliance). Sleep onset, midpoint of sleep, and the µMCTQ-derived marker of chronotype showed slight deviations toward earlier times in the µMCTQ when compared with the stdMCTQ (<35 min). The µMCTQ assessment of chronotype showed good test-retest reliability and correlated significantly with phase markers from actimetry and melatonin (DLMO), especially with measurements taken on work-free days. Because of its brevity, the µMCTQ represents an ideal tool to estimate individual internal time in time-critical contexts, from large cohort studies to individualized medicine.
Previous caesarean section is associated with lower subsequent in vitro fertilization live birth rates

Abstract This retrospective cohort study examines the association between previous mode of delivery and subsequent live birth rate in women who become pregnant after in vitro fertilization (IVF) or intra cytoplasmic sperm injection (ICSI) after their first delivery. The study included 112 women with a previous caesarean section and 418 women with a previous vaginal delivery, and a total of 1588 embryo transfers between January 2005 and June 2016 (Leiden University Medical Centre, the Netherlands). The mean age was 35 years and mean number of embryos transferred per attempt, 1.18. The study population included a total of 429 pregnancies resulting in 296 live births. The crude odds ratio for a subsequent live birth per embryo transfer was 0.60 (CI; 0.44 to 0.83, p = 0.002) in women with a previous caesarean section compared to women with a previous vaginal delivery. After adjustment for age, fresh/frozen-thawed embryo transfer and quality of the embryo, the odds ratio was 0.64 (CI; 0.46 to 0.89, p = 0.01). It was concluded that in subfertile women trying to achieve a subsequent pregnancy with IVF or ICSI, a history of caesarean section was associated with a reduced live birth rate per embryo transfer compared to women with a history of one previous vaginal delivery.
Beyond inflammasomes: emerging function of gasdermins during apoptosis and NETosis

Programmed cell death is a key mechanism involved in several biological processes ranging from development and homeostasis to immunity, where it promotes the removal of stressed, damaged, malignant or infected cells. Abnormalities in the pathways leading to initiation of cell death or removal of dead cells are consequently associated with a range of human diseases including infections, autoinflammatory disease, neurodegenerative disease and cancer. Apoptosis, pyroptosis and NETosis are three well‐studied modes of cell death that were traditionally believed to be independent of one another, but emerging evidence indicates that there is extensive cross‐talk between them, and that all three pathways can converge onto the activation of the same cell death effector—the pore‐forming protein Gasdermin D (GSDMD). In this review, we highlight recent advances in gasdermin research, with a particular focus on the role of gasdermins in pyroptosis, NETosis and apoptosis, as well as cell type‐specific consequences of gasdermin activation. In addition, we discuss controversies surrounding a related gasdermin family protein, Gasdermin E (GSDME), in mediating pyroptosis and secondary necrosis following apoptosis, chemotherapy and inflammasome activation.
Factors influencing the functional outcomes of tibia plateau fractures after surgical fixation

Aims: The aim of this study is to assess the functional and radiological outcomes of 52 surgically treated tibial plateau fractures and to determine the factors affecting functional outcomes. Subjects and Methods: A total of 52 patients who were operated between 2007 and 2014 due to tibial plateau fractures were retrospectively reviewed. The Knee Society Score (KSS) was used for the functional outcome assessment. The Kellgren–Lawrence radiological evaluation score was used for the relationship between postoperative trauma and osteoarthritis in the last follow-up. Results: Patients' mean age was 47.7 years (range, 14–84 years). The immobilization period was 4.2 weeks (range, 0–8 weeks), the full weightbearing time was 3.3 months (range, 1.5–5 months), and the follow-up time was 47 months (range, 17–102 months). Patients' mean KSS was 84.3 (range, 40–100). According to the Kellgren–Lawrence classification, 26 patients had grade 0, 11 patients had grade 1, 8 patients had grade 2, 5 patients had grade 3, and 2 patients had grade 4 postoperative osteoarthritis. Conclusion: Use of graft if there is collapse on joint surface, early knee motion, and early started full weightbearing after surgical fixation of tibial plateau fracture is essential for successful outcome. Findings of osteoarthritis on X-rays are not related to poor functional outcome at the mid- to long-term follow-up of surgical treated tibial plateau fractured patients.
Non-Catalytic Subunits Facilitate Quaternary Organization of Plastidic Acetyl-CoA Carboxylase1[OPEN]

Non-catalytic subunits of the heteromeric acetyl-CoA carboxylase facilitate the assembly of an activate enzyme and hence accelerate the ability to generate the key precursor of fatty acid biosynthesis, malonyl-CoA. Arabidopsis (Arabidopsis thaliana), like most dicotyledonous plants, expresses a multicomponent, heteromeric acetyl-CoA carboxylase (htACCase), which catalyzes the generation of the malonyl-CoA precursor of de novo fatty acid biosynthesis. This enzyme consists of four catalytic subunits: biotin carboxylase (BC), carboxyltransferase (CT)-α, CT-β, and biotin carboxyl carrier protein (BCCP1 or BCCP2). By coexpressing combinations of components in a bacterial expression system, we demonstrate noncatalytic BADCs facilitate the assembly and activation of BCCP–BADC–BC subcomplexes catalyzing the bicarbonate-dependent hydrolysis of ATP, which is the first half-reaction catalyzed by the htACCase enzyme. Although BADC proteins do not directly impact formation of the CT–αβ subcomplex, the BADC-facilitated BCCP–BADC–BC subcomplex can more readily interact with the CT–αβ subcomplex to facilitate the generation of malonyl-CoA. The Arabidopsis genome encodes three BADC isoforms (BADC1, BADC2, and BADC3), and BADC2 and BADC3 (rather than BADC1), in combination with BCCP1, best support this quaternary-structural organization and catalytic activation of the htACCase enzyme. Physiological genetic studies validate these attributes as Arabidopsis double mutants singularly expressing BADC2, BADC3, or BADC1 present increasingly greater deleterious impacts on morphological and biochemical phenotypes. Specifically, plants expressing only BADC2 develop normally, plants only expressing BADC3 suffer a stunted root-growth phenotype, and plants expressing only BADC1 are embryo-lethal. The latter phenotype may also be associated with the distinct suborganelle localization of BADC1 in plastids as compared to the localization of the other two BADC homologs. These finding can inspire novel strategies to improve the biological sources of fats and oils for dietary and industrial applications.
On the Interplay Between Charge-Shift Bonding and Halogen Bonding.

The nature of halogen-bond interactions has been analysed from the perspective of the astatine element, which is potentially the strongest halogen-bond donor. Relativistic quantum calculations on complexes formed between halide anions and a series of Y3C-X (Y = F to X, X = I, At) halogen-bond donors disclosed unexpected trends, e.g. , At3C-At revealing a weaker donating ability than I3C-I despite a stronger polarizability. All the observed peculiarities have their origin in a specific component of C-Y bonds: the charge-shift bonding. Descriptors of the Quantum Chemical Topology show that the halogen-bond strength can be quantitatively anticipated from the magnitude of charge-shift bonding operating in Y3C-X. The charge-shift mechanism weakens the ability of the halogen atom X to engage in halogen bonds. This outcome provides rationales for outlier halogen-bond complexes, which are at variance with the consensus that the halogen-bond strength scales with the polarizability of the halogen atom.
The prevalence and causes of wrong tooth extraction

Background: Dental extraction is a common procedure that is subject to complications and errors including extraction of the wrong tooth. This study aimed to determine the prevalence and identify the causes of wrong tooth extractions and explore the attitude of dentists after extraction of a wrong tooth. Methods: A questionnaire was adapted to fit the needs of this project and was distributed among all the dentists in four teaching dental clinics. The questionnaire was available in both the English and Arabic languages. Results: Of the 486 questionnaires, 186 questionnaires were returned (response rate of 37%) and used for the analysis. The prevalence of wrong tooth extraction was 21.1%. The three most common reasons for extracting a wrong tooth were miscommunication (31.6%), inadequate referral (28.9%), and exhaustion of an overworked dentist (28.9%). Surprisingly, only 50% informed the patient and documented the incident in the patient's chart. Few dentists apologized to their patients or offered any kind of solution or compensation. Conclusion: Wrong tooth extraction is a prevalent yet preventable problem. Most of the common causes of this problem appear to be more system rather than individual related. There is a pressing need to implement the universal protocol for the prevention of wrong site, wrong procedure, and wrong person surgery.
Reprogramming: identifying the mechanisms that safeguard cell identity

ABSTRACT Development and homeostasis rely upon concerted regulatory pathways to establish the specialized cell types needed for tissue function. Once a cell type is specified, the processes that restrict and maintain cell fate are equally important in ensuring tissue integrity. Over the past decade, several approaches to experimentally reprogram cell fate have emerged. Importantly, efforts to improve and understand these approaches have uncovered novel molecular determinants that reinforce lineage commitment and help resist cell fate changes. In this Review, we summarize recent studies that have provided insights into the various chromatin factors, post-transcriptional processes and features of genomic organization that safeguard cell identity in the context of reprogramming to pluripotency. We also highlight how these factors function in other experimental, physiological and pathological cell fate transitions, including direct lineage conversion, pluripotency-to-totipotency reversion and cancer. Summary: Recent work has characterized barriers to cell fate change. This Review explores the possibility that these barriers play a role during alternative cell fate transitions as well as in tumorigenesis.