Miracle-dz/UniFAR-FTUs huggingface dataset:
Measles and rubella seroimmunity in newly arrived adult immigrants in Sweden

Abstract Background: International migrants could be considered as a risk group for being susceptible to vaccine preventable diseases such as measles and rubella. However, data on immunity in different migrant groups are scarce. Apart from asylum seekers and refugees, other immigrant groups might also be at risk. We have examined measles and rubella specific IgG antibodies among newly arrived adult immigrants in Skåne region in southern Sweden. In contrast to children, adult immigrants are not offered catch-up vaccinations after arrival. Methods: Stored serum samples from 989 asylum seekers and 984 pregnant women from the antenatal screening program, who had recently settled in Sweden, were analyzed for specific measles and rubella IgG-antibodies. Sex, age, reason for screening and geographic origin were variables entered into a multivariate regression model. Results: There were considerable differences in seroimmunity to measles with regard to geographic origin (44–97%). Measles seroimmunity gaps were most prominent in immigrants from some European regions such as the Baltic countries, the former Yugoslavia and the Newly Independent States and Russia. Seroprotection for rubella varied less between geographic regions (90–99%). Conclusion: Susceptibility to measles among adult immigrants arriving in Sweden varies considerably depending on their geographic origin. Vaccinations against measles and rubella should be offered to groups of immigrants who might be incompletely immunized.
Adenocarcinoma of the Rete Testis: Clinicopathologic and Immunohistochemical Characterization of 6 Cases and Review of the Literature

Adenocarcinoma of the rete testis is rare and its etiological and pathologic characteristics are not well studied. We therefore investigated the clinical, morphologic, and immunohistochemical features of 6 cases diagnosed at our institution and conducted a detailed review of the literature. The mean age was 64 years. All patients presented with testicular masses; 4 were right-sided. On gross examination, all tumors were centered in the hilum and had solid and cystic cut surfaces. Microscopically, all had intrarete and invasive growth and showed multiple patterns, with a variable proportion of papillary, solid and glandular morphology, the latter varying from slit-like lumens to well-formed glands and tubules. Less common patterns included corded/trabecular (n=3), cribriform (n=3), glomeruloid (n=3), nested (n=2), and micropapillary (n=2). Discrete nests of eosinophilic and clear cells were a distinctive feature in 3 cases. Geographic necrosis occurred in 3 cases. All showed at least moderate nuclear pleomorphism with ovoid nuclei. Transition from benign to malignant rete epithelium was seen in all cases. The stroma was hyalinized to partially fibrotic. On immunohistochemical study, the tumor cells were positive for CK7 (5/5), AE1/AE3 cytokeratin (5/5), EMA (5/5), vimentin (5/5), EpCAM (detected by BerEP4 anitbody) (4/5), CK5/6 (4/5), nuclear Wilms Tumor-1 (4/5), epithelial specific antigen (detected by MOC31 antibody) (3/4), PAX8 (3/5), and calretinin (2/5). OCT3/4, SALL4, CD30, NKX3.1, PSA, &agr;-inhibin, CK20, and S100 protein were negative. Ki-67 proliferative index ranged from 5% to 60% (mean: 40, median: 43). At presentation, 5 patients had retroperitoneal lymph node metastasis and one of these also had pulmonary metastases. The sixth patient developed pulmonary metastasis within 15 months of diagnosis. Three died within 4 years of diagnosis. In summary, adenocarcinoma of the rete testis is a rare malignant tumor with poor survival and a high propensity for retroperitoneal lymph node metastasis that must be distinguished from other testicular neoplasms and metastasis to the testis. Hilar localization, transition from benign to malignant rete epithelium, and supportive immunostains aid its accurate diagnosis.
Retrospective Analysis of False-Positive and Disputed Rifampin Resistance Xpert MTB/RIF Assay Results in Clinical Samples from a Referral Hospital in Hunan, China

Concerns about the specificity of the Xpert MTB/RIF (Xpert) assay have arisen, as false-positive errors in the determination of Mycobacterium tuberculosis complex (MTBC) infection and rifampin (RIF) resistance in clinical practice have been reported. Here, we investigated 33 cases where patients were determined to be RIF susceptible using the Bactec MGIT 960 (MGIT) culture system but RIF resistant using the Xpert assay. ABSTRACT Concerns about the specificity of the Xpert MTB/RIF (Xpert) assay have arisen, as false-positive errors in the determination of Mycobacterium tuberculosis complex (MTBC) infection and rifampin (RIF) resistance in clinical practice have been reported. Here, we investigated 33 cases where patients were determined to be RIF susceptible using the Bactec MGIT 960 (MGIT) culture system but RIF resistant using the Xpert assay. Isolates from two of these patients were found not to have any mutations in the rifampin resistance determining region (RRDR) region of rpoB and had good treatment outcomes with first-line antituberculosis (anti-TB) drugs. The remaining 31 patients included 5 new cases and 26 previously treated patients. A large number of well-documented disputed mutations, including Leu511Pro, Asp516Tyr, His526Asn, His526Leu, His526Cys, and Leu533Pro, were detected, and mutations, including a 508 to 509 deletion and His526Gly, were described here as disputed mutations for the first time. Twenty-one (81%) of the 26 previously treated patients had poor treatment outcomes, and isolates from 19 (90%) of these 21 patients were resistant to isoniazid (INH) as determined using the MGIT culture system. Twenty-seven of the 31 isolates with disputed rpoB mutations were phenotypically resistant to INH, 21 (78%) being predicted by GenoType MTBDRplus to have a high level of INH resistance. Most (77.4%) of the isolates with disputed mutations were of the Beijing lineage. These findings have implications for the interpretation of false-positive and disputed rifampin resistance Xpert MTB/RIF results in clinical samples and provide guidance on how clinicians should manage patients carrying isolates with disputed rpoB mutations.
Emotional Distraction in the Context of Memory-Based Orienting of Attention

Attention can be guided by expectations stemming from long-term memories. In addition to such endogenous cues, exogenous salient stimuli capture attention, such as those conveying threat. This study examined the extent to which threatening distractors affect the employment of memories in guiding attention, and whether this is affected by trait anxiety. Emotional distractors were incorporated into a speeded target detection task, in which memory cues were presented simultaneously with task irrelevant emotional faces. Fearful face distractors disrupted target detection significantly more than neutral faces and the additional disruption to task performance from fearful compared with neutral faces was positively correlated with trait anxiety scores. The current findings of attentional capture by threat in the context of a second, powerful endogenous driver of attention underscore the magnitude of anxiety-related attention to threat. That is, threatening stimuli are sufficiently salient to induce prolonged disruption to goal directed behavior in anxious individuals.
Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium

Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.
Antibody-functionalized gold nanoparticles as tumor-targeting radiosensitizers for proton therapy.

AIM This study aimed at developing antibody-functionalized gold nanoparticles (AuNPs) to selectively target cancer cells and probing their potential radiosensitizing effects under proton irradiation. MATERIALS & METHODS AuNPs were conjugated with cetuximab (Ctxb-AuNPs). Ctxb-AuNP uptake was evaluated by transmission electron microscopy and atomic absorption spectroscopy. Radioenhancing effect was assessed using conventional clonogenic assay. RESULTS & CONCLUSION Ctxb-AuNPs specifically bound to and accumulated in EGFR-overexpressing A431 cells, compared with EGFR-negative MDA-MB-453 cells. Ctxb-AuNPs enhanced the effect of proton irradiation in A431 cells but not in MDA-MB-453 cells. These data indicate, for the first time, that combining enhanced uptake by specific targeting and radioenhancing effect, using conjugated AuNPs, is a promising strategy to increase cell killing by protontherapy.
The Interpersonal Neurobiology of Child Maltreatment: Parasympathetic Substrates of Interactive Repair in Maltreating and Nonmaltreating Mother–Child Dyads

Children’s repair of conflict with parents may be particularly challenging in maltreating families, and early, stressful parent–child interactions may contribute to children’s altered neurobiological regulatory systems. To explore neurobiological signatures of repair processes, we examined whether mother and child individual and dyadic respiratory sinus arrhythmia (RSA) covaried with interactive repair differently in maltreating versus nonmaltreating mother–preschooler dyads (N = 101), accounting for whether repair was mother or child initiated. Mother-initiated repair was equally frequent and protective across groups, associated with no change in mother or child RSA at higher levels of repair. But lower levels of mother repair were associated with child RSA withdrawal in nonmaltreating dyads versus child RSA augmentation in maltreating dyads. In maltreating dyads only, higher child-initiated repair was associated with higher mean mother RSA, whereas lower child repair was associated with mother RSA withdrawal. Findings suggest that interactive repair may have a buffering effect on neurobiological regulation but also that maltreating mothers and children show atypical neurobiological response to interpersonal challenges including differences related to children conducting the work of interactive repair that maltreating parents are less able to provide. We conclude by considering the role of maladaptive parent–child relationship processes in the biological embedding of early adversity.
A Genetic Algorithm for Stochastic Inversion in Contaminant Subsurface Hydrology

Identifying the spatial distribution of hydrological properties of aquifers is a key problem in subsurface hydrology. The aquifer structure plays an important role in contaminant transport. Identifying the properties (primarily the hydraulic conductivity) is essentially an inversion problem that is ill‐posed, non‐unique and computationally intensive by definition. In this work, the non‐uniqueness of the inverse problem is tackled via a novel Genetic Algorithm approach combined with a geostatistical method (Sequential Indicator Simulations) for construction of realizations of properties spatial distributions, which are modeled as random. The Genetic Algorithm cross‐over operator is based on a novel concept of pilot‐planes: daughter realizations adopt pilot‐planes from one of their parents. In addition, each aquifer realization is conditioned on the geological hard data and is constructed by sampling the facies distribution, evaluated by indicator variograms. The approach is illustrated in two test cases: a synthetic two‐dimensional (2D) case and an actual three‐dimensional (3D) case. The results have shown the ability of the proposed approach to generate a set of realizations, where each individual exhibits minor deviations from the measurements. Further, a comparison between the proposed approach and direct (Monte Carlo) approach shows that the Genetic Algorithm was able to generate an ensemble of solutions with a better fitting of the measurements than the direct approach by a significantly reduced computational effort.
The Head Down Generation: Musculoskeletal Symptoms and the Use of Smartphones Among Young University Students.

BACKGROUND Smartphones offer a variety of mobile applications for diverse purposes and access to services that contribute to an increased time of interaction with the device, influencing the users' health and behavior. INTRODUCTION The time of interaction with smartphones is more intense with the younger generation, and physical, psychological, and social complications are reported. This research aims at identifying the factors associated with musculoskeletal symptoms due to the use of smartphones in university students in Brazil. MATERIALS AND METHODS The study has a quantitative transversal type approach, with 522 college students between the ages 18 and 26. A structured questionnaire was applied in 2017, to characterize the sociodemographic profile, composed of information regarding the use of smartphones added to the Nordic questionnaire of musculoskeletal symptoms. RESULTS One of the main results found was a tendency for participants to have symptoms of musculoskeletal pain with regards to their typing methods on smartphones. When asked about the cases when such symptoms were considered to be related to the use of the device, most cited the cervical region (43.87% of cases). It was also found that those who type on their phones with the head at 45° and 60° angles are about twice as likely to have higher scores of severe symptoms than those typing with their neck at 0° (anatomical position). CONCLUSION Within the university student population the typing position on a smartphone and time of use are associated with the presence of pain in the cervical region.
What is the real cardiac anatomy?

The heart is a remarkably complex organ. Teaching its details to medical students and clinical trainees can be very difficult. Despite the complexity, accurate recognition of these details is a pre‐requisite for the subsequent understanding of clinical cardiologists and cardiac surgeons. A recent publication promoted the benefits of virtual reconstructions in facilitating the initial understanding achieved by medical students. If such teaching is to achieve its greatest value, the datasets used to provide the virtual images should themselves be anatomically accurate. They should also take note of a basic rule of human anatomy, namely that components of all organs should be described as they are normally situated within the body. It is almost universal at present for textbooks of anatomy to illustrate the heart as if removed from the body and positioned on its apex, the so‐called Valentine situation. In the years prior to the emergence of interventional techniques to treat cardiac diseases, this approach was of limited significance. Nowadays, therapeutic interventions are commonplace worldwide. Advances in three‐dimensional imaging technology, furthermore, now mean that the separate components of the heart can readily be segmented, and then shown in attitudinally appropriate fashion. In this review, we demonstrate how such virtual dissection of computed tomographic datasets in attitudinally appropriate fashion reveals the true details of cardiac anatomy. The virtual approach to teaching the arrangement of the cardiac components has much to commend it. If it is to be used, nonetheless, the anatomical details on which the reconstructions are based must be accurate. Clin. Anat. 32:288–309, 2019. © 2019 The Authors. Clinical Anatomy published by Wiley Periodicals, Inc. on behalf of American Association of Clinical Anatomists.
Microstate functional connectivity in EEG cognitive tasks revealed by a multivariate Gaussian hidden Markov model with phase locking value

Objective. Tracking the spatiotemporal fast (~100 ms) transient networks remains challenging due to a limited understanding of neural activity dynamics as well as a lack of relevant sophisticated methodologies. In this study, we introduce a novel approach to identify simultaneously distinct EEG microstates and their corresponding microstate functional connectivity (µFC) networks in which each µFC network is associated with a distinguished connectivity pattern of recurrent neuronal activity. Approach. The introduced approach is based on a multivariate Gaussian hidden Markov model (MGHMM) to decompose the sensor-space stochastic multi-subject event-related potential (ERP) into quasi-stable EEG microstates. Raw trial segments whose time windows belong to a corresponding segmented EEG microstate are then concatenated for measuring their µFC using the time-averaged phase-locking value. Illustration of this method is evaluated with synthetic data for which ground-truth microstate dynamics are known. Furthermore, we apply the method to identify EEG microstates and corresponding µFC networks in publicly available EEG data measured from visual cognitive tasks. Finally, we compare the MGHMM method with conventional dynamic FC (dFC) approaches using clustering-based K-means and time sliding windows, which conversely segregate the macrostate FC matrices across times into ‘FC-states’. Main results. By using the MGHMM approach, we reveal: (1) EEG microstates, (2) µFC networks, (3) the associations of EEG microstate networks and their corresponding µFC networks dynamically modulated in publicly available EEG cognitive tasks, and (4) compared dFC performances between our proposed µFC approaches and ‘FC-states’ segmented by clustering-based K-means and time sliding windows. Significance. Evidence of significant improvements of microstate correlations (p -value < 0.05) and improved tendency of FC distinction (p -value = 0.064) over reported methods with simulated and realistic data will make this approach a preferred methodology to study dynamic brain networks and guarantee its use for further clinical applications.
Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

Significance Studying the organization of genes within genomes across broad evolutionary timescales can advance our understanding of the evolution of traits and clades. We have used a network approach to investigate genome dynamics of mammals and angiosperms. In general, genome organization and gene microcollinearity is much more conserved in mammals than in flowering plants. We then identified the genomic outliers or “rebel genes,” within each clade. Genes that have moved are unusual for mammals, whereas highly conserved single-copy genes are exceptional for plants. How conservation and changes in synteny or fundamental differences in genome organization have contributed to the evolution of lineages could be a new scientific frontier. A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.
First Laboratory-Confirmed Outbreak of Human and Animal Rift Valley Fever Virus in Uganda in 48 Years

Abstract. In March 2016, an outbreak of Rift Valley fever (RVF) was identified in Kabale district, southwestern Uganda. A comprehensive outbreak investigation was initiated, including human, livestock, and mosquito vector investigations. Overall, four cases of acute, nonfatal human disease were identified, three by RVF virus (RVFV) reverse transcriptase polymerase chain reaction (RT-PCR), and one by IgM and IgG serology. Investigations of cattle, sheep, and goat samples from homes and villages of confirmed and probable RVF cases and the Kabale central abattoir found that eight of 83 (10%) animals were positive for RVFV by IgG serology; one goat from the home of a confirmed case tested positive by RT-PCR. Whole genome sequencing from three clinical specimens was performed and phylogenetic analysis inferred the relatedness of 2016 RVFV with the 2006–2007 Kenya-2 clade, suggesting previous introduction of RVFV into southwestern Uganda. An entomological survey identified three of 298 pools (1%) of Aedes and Coquillettidia species that were RVFV positive by RT-PCR. This was the first identification of RVFV in Uganda in 48 years and the 10th independent viral hemorrhagic fever outbreak to be confirmed in Uganda since 2010.