Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.

OBJECTIVES Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late17th to early18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America. MATERIALS AND METHODS Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence. RESULTS Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa. DISCUSSION Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late17th century.
Markerless Augmented Reality via Stereo Video See-Through Head-Mounted Display Device

Conventionally, the camera localization for augmented reality (AR) relies on detecting a known pattern within the captured images. In this study, a markerless AR scheme has been designed based on a Stereo Video See-Through Head-Mounted Display (HMD) device. The proposed markerless AR scheme can be utilized for medical applications such as training, telementoring, or preoperative explanation. Firstly, a virtual model for AR visualization is aligned to the target in physical space by an improved Iterative Closest Point (ICP) based surface registration algorithm, with the target surface structure reconstructed by a stereo camera pair; then, a markerless AR camera localization method is designed based on the Kanade-Lucas-Tomasi (KLT) feature tracking algorithm and the Random Sample Consensus (RANSAC) correction algorithm. Our AR camera localization method is shown to be better than the traditional marker-based and sensor-based AR environment. The demonstration system was evaluated with a plastic dummy head and the display result is satisfactory for a multiple-view observation.
Measuring psychological inflexibility in adult and child hearing loss

Abstract Objective: Hearing loss is a chronic condition that impacts functioning among individuals with hearing loss and caregivers of children with hearing loss. Even though treatments for hearing loss can alleviate functional impairment, psychological factors like psychological inflexibility may interfere with treatment engagement and adherence, undermining the benefits of treatment. Measuring psychological inflexibility may inform care providers’ case conceptualisation, improving the quality and precision of audiological interventions. Thus, this study aimed to develop and validate measures of psychological inflexibility in hearing loss for adults and caregivers of children with hearing loss. Design: Participants were invited to complete an online survey. Study samples: Our sample comprised adults with hearing loss (N = 264) and primary caregivers of children with hearing loss (N = 275). Results: The final versions of Acceptance and Action Questionnaire-Adult Hearing Loss (AAQ-AHL) and Acceptance and Action Questionnaire-Management of Child Hearing Loss (AAQ-MCHL) showed good to excellent internal reliability and concurrent and discriminant validity. Conclusion: Although the AAQ-AHL and AAQ-MCHL showed acceptable psychometric properties, more tests are needed to further validate these measures and verify their utility in research and clinical settings.
Assessment of the interplay between scaffold geometry, induced shear stresses, and cell proliferation within a packed bed perfusion bioreactor

By favoring cell proliferation and differentiation, perfusion bioreactors proved efficient at optimizing cell culture. The aim of this study was to quantify cell proliferation within a perfusion bioreactor and correlate it to the wall shear stress (WSS) distribution by combining 3‐D imaging and computational fluid dynamics simulations.NIH‐3T3 fibroblasts were cultured onto a scaffold model made of impermeable polyacetal spheres or Polydimethylsiloxane cubes. After 1, 2, and 3 weeks of culture, constructs were analyzed by micro‐computed tomography (μCT) and quantification of cell proliferation was assessed. After 3 weeks, the volume of cells was found four times higher in the stacking of spheres than in the stacking of cube.3D‐μCT reconstruction of bioreactors was used as input for the numerical simulations. Using a lattice‐Boltzmann method, we simulated the fluid flow within the bioreactors. We retrieved the WSS distribution (PDF) on the scaffolds surface at the beginning of cultivation and correlated this distribution to the local presence of cells after 3 weeks of cultivation. We found that the WSS distributions strongly differ between spheres and cubes even if the porosity and the specific wetted area of the stackings were very similar. The PDF is narrower and the mean WSS is lower for cubes (11 mPa) than for spheres (20 mPa). For the stacking of spheres, the relative occupancy of the surface sites by cells is maximal when WSS is greater than 20 mPa. For cubes, the relative occupancy is maximal when the WSS is lower than 10 mPa. The discrepancies between spheres and cubes are attributed to the more numerous sites in stacking of spheres that may induce 3‐D (multi‐layered) proliferation.
Association between PTEN and clinical-pathological features of osteosarcoma

Previous studies indicated the prognostic value of phosphatase and tensin homolog deleted on chromosome ten (PTEN) in osteosarcoma (OS). There was a great degree of inconsistency between these reports. The aim of this meta-analysis was to investigate the clinicopathological features and prognostic role of PTEN positive expression on OS. We searched NCBI PubMed, Embase, Springer, ISI Web of Knowledge, the Cochrane library, China National Knowledge Internet database (CNKI), Wanfang database, Chinese VIP database and Chinese Biological Medical Database (CBM) for relevant papers published before 28 November 2018. The eligibility of all retrieved studies assessing the relationship between PTEN expression and clinicopathological and prognostic outcomes in OS were incorporated. Pooled odds ratio (OR) and 95% confidence intervals (CIs) were used to estimate the outcomes. A total of 13 studies with 580 OS patients were involved to assess the relationship between PTEN expression and clinicopathological features of OS. PTEN positive expression was significantly associated with male (OR = 1.57, 95% CI: 1.03–2.38, P=0.035<0.05) and OS high differentiation (OR = 2.33, 95% CI: 1.26–4.29, P=0.007<0.05). Additionally, positive expressions of PTEN predict no neoplasm metastasis (OR = 5.69, 95% CI: 3.64–8.90, P<0.05). The results of our study showed that positive expression of PTEN may predict higher 5-year survival in OS with the pooled OR of 8.73 (95% CI: 4.18–18.24, P<0.05). The results from the present study suggest that positive expression of PTEN is significantly associated with male, high differentiation, no metastasis and high 5-year overall survival rate in OS.
STAT5a/b Deficiency Delays, but does not Prevent, Prolactin-Driven Prostate Tumorigenesis in Mice

The canonical prolactin (PRL) Signal Transducer and Activator of Transcription (STAT) 5 pathway has been suggested to contribute to human prostate tumorigenesis via an autocrine/paracrine mechanism. The probasin (Pb)-PRL transgenic mouse models this mechanism by overexpressing PRL specifically in the prostate epithelium leading to strong STAT5 activation in luminal cells. These mice exhibit hypertrophic prostates harboring various pre-neoplastic lesions that aggravate with age and accumulation of castration-resistant stem/progenitor cells. As STAT5 signaling is largely predominant over other classical PRL-triggered pathways in Pb-PRL prostates, we reasoned that Pb-Cre recombinase-driven genetic deletion of a floxed Stat5a/b locus should prevent prostate tumorigenesis in so-called Pb-PRLΔSTAT5 mice. Anterior and dorsal prostate lobes displayed the highest Stat5a/b deletion efficiency with no overt compensatory activation of other PRLR signaling cascade at 6 months of age; hence the development of tumor hallmarks was markedly reduced. Stat5a/b deletion also reversed the accumulation of stem/progenitor cells, indicating that STAT5 signaling regulates prostate epithelial cell hierarchy. Interestingly, ERK1/2 and AKT, but not STAT3 and androgen signaling, emerged as escape mechanisms leading to delayed tumor development in aged Pb-PRLΔSTAT5 mice. Unexpectedly, we found that Pb-PRL prostates spontaneously exhibited age-dependent decline of STAT5 signaling, also to the benefit of AKT and ERK1/2 signaling. As a consequence, both Pb-PRL and Pb-PRLΔSTAT5 mice ultimately displayed similar pathological prostate phenotypes at 18 months of age. This preclinical study provides insight on STAT5-dependent mechanisms of PRL-induced prostate tumorigenesis and alternative pathways bypassing STAT5 signaling down-regulation upon prostate neoplasia progression.
Human Bocavirus Infection in Adults: Clinical Features and Radiological Findings

Objective Human bocavirus (HBoV) is a newly identified pathogen that can cause upper and lower respiratory infections usually in children; however, its clinical characteristics and significance in respiratory infections in adults have not been well known. Our objective was to evaluate the clinical features of respiratory HBoV infection and to describe the CT findings of HBoV pneumonia in adults. Materials and Methods A total of 185 adult patients diagnosed with HBoV infection at a tertiary referral center between January 2010 and December 2017 were retrospectively evaluated with respect to the clinical characteristics of HBoV infection and its risk factors for pneumonia. Chest CT findings for 34 patients with HBoV pneumonia without co-infection were analyzed and compared between immunocompetent (n = 18) and immunocompromised (n = 16) patients. Results HBoV infections were predominantly noted between February and June. Among the 185 patients with HBoV infection, 119 (64.3%) had community-acquired infections and 110 (59.5%) had pneumonia. In multivariable analysis, older age (odds ratio [OR], 1.02; 95% confidence interval [CI], 1.00–1.04; p = 0.045) and nosocomial infection (OR, 2.07; 95% CI, 1.05–4.10; p = 0.037) were associated with HBoV pneumonia. The main CT findings were bilateral consolidation (70.6%) and/or ground-glass opacities (64.7%); centrilobular nodules (14.7%) were found less frequently. The pattern of CT findings were not significantly different between immunocompetent and immunocompromised patients (all, p > 0.05). Conclusion HBoV infection can be a potential respiratory tract infection in adults. The most frequent CT findings of HBoV pneumonia were bilateral consolidation and/or ground-glass opacities.
Segregation of speakers for speech recognition and speaker identification

A method for segregating speech from speakers engaged in dialogs is described. The method, assuming no prior knowledge of the speakers, employs a distance measure between speech segments used in conjunction with a clustering algorithm to perform the segregation. Properties of the distance measure are discussed, and an air traffic control application is described. <<ETX>>
Genetic Aberrations Associated with Photodynamic Therapy in Colorectal Cancer Cells

Photodynamic therapy (PDT) is a cancer treatment modality that utilizes three components: light (λ 650–750 nm), a photosensitizer (PS) and molecular oxygen, which upon activation renders the modality effective. Colorectal cancer has one of the highest incident rates as well as a high mortality rate worldwide. In this study, a zinc (Zn) metal-based phthalocyanine (ZnPcSmix) PS was used to determine its efficacy for the treatment of colon adenocarcinoma cells (DLD-1 and Caco-2). Photoactivation of the PS was achieved by laser irradiation at a wavelength of 680 nm. Dose responses were performed to establish optimal PS concentration and irradiation fluence. A working combination of 20 µM ZnPcSmix and 5 J/cm2 was used. Biochemical responses were determined after 1 or 24 h incubation post-treatment. Since ZnPcSmix is localized in lysosomes and mitochondria, mitochondrial destabilization analysis was performed monitoring mitochondrial membrane potential (MMP). Cytosolic acidification was determined measuring hydrogen peroxide (H2O2) levels in the cytoplasm. Having established apoptotic cell death induction, an apoptosis PCR array was performed to establish the apoptotic mechanism. In DLD-1 cells, expression of genes included 3 up-regulated and 20 down-regulated genes while in Caco-2 cells, there were 16 up-regulated and 22 down-regulated genes. In both cell lines, in up-regulated genes, there was a combination of pro- and anti-apoptotic genes that were significantly expressed. Gene expression results showed that more tumorigenic cells (DLD-1) went through apoptosis; however, they exhibit increased risk of resistance and recurrence, while less tumorigenic Caco-2 cells responded better to PDT, thus being suggestive of a better prognosis post-PDT treatment. In addition, the possible apoptotic mechanisms of cell death were deduced based on the genetic expression profiling of regulatory apoptotic inducing factors.
Lipid-Rich Necrotic Core of Basilar Artery Atherosclerotic Plaque: Contrast-Enhanced Black Blood Imaging on Vessel Wall Imaging

Purpose: We wished to evaluate the lipid-rich necrotic core (LRNC) using contrast-enhanced T1-weighted (CE-T1W) black-blood (BB) imaging for vessel walls. Methods: Ninety-five patients with basilar artery (BA) stenosis who underwent magnetic resonance angiography between January 2016 and August 2018 were enrolled into this present study. CE-T1W BB imaging was considered as a reference method for identifying an LRNC. Results: Ten (10.5%) patients were identified as having an LRNC on CE-T1W BB imaging. Of these patients, 9 had acute symptoms. The extent of stenosis in patients with an LRNC on CE-T1W BB imaging was significantly greater than that of patients without an LRNC (p < 0.001). The maximum wall thickness in patients with an LRNC on CE-T1W imaging was significantly thicker than that of patients without an LRNC (p = 0.008). Conclusions: Identification of an LRNC on CE-T1W BB imaging was associated with high-grade stenosis and massive plaque burden from BA atherosclerosis.
Distortion correction for high‐resolution single‐shot EPI DTI using a modified field‐mapping method

The widely used single‐shot EPI (SS‐EPI) diffusion tensor imaging (DTI) suffers from strong image distortion due to B0 inhomogeneity, especially for high‐resolution imaging. Traditional methods such as the field‐mapping method and the top‐up method have various deficiencies in high‐resolution SS‐EPI DTI distortion correction. This study aims to propose a robust distortion correction approach, which combines the advantages of traditional methods and overcomes their deficiencies, for high‐resolution SS‐EPI DTI.
ProtDCal‐Suite: A web server for the numerical codification and functional analysis of proteins

Computational tools for the analysis of protein data and the prediction of biological properties are essential in life sciences and biomedical research. Here, we introduce ProtDCal‐Suite, a web server comprising a set of machine learning‐based methods for studying proteins. The main module of ProtDCal‐Suite is the ProtDCal software. ProtDCal translates the structural information of proteins into numerical descriptors that serve as input to machine‐learning techniques. The ProtDCal‐Suite server also incorporates a post‐processing optional stage that allows ranking and filtering the obtained descriptors by computing their Shannon entropy values across the input set of proteins. ProtDCal's codification was used in the development of models for the prediction of specific protein properties. Thus, the other modules of ProtDCal‐Suite are protein analysis tools implemented using ProtDCal's descriptors. Among them are PPI‐Detect, for predicting the interaction likelihood of protein–protein and protein–peptide pairs, Enzyme Identifier, for identifying enzymes from amino acid sequences or 3D structures, and Pred‐NGlyco, for predicting N‐glycosylation sites. ProtDCal‐Suite is freely accessible at https://protdcal.zmb. uni‐due.de.
Patient and Disease Characteristics Associate With Sensory Testing Results in Chronic Pancreatitis

Background: Abdominal pain is the most common symptom in chronic pancreatitis (CP) and has an extensive impact on patients’ lives. Quantitative sensory testing (QST) provides information on sensitivity to pain and mechanisms that can help quantify pain and guide treatment. The aims of this study were (1) to explore sensitivity to pain in patients with CP using QST and (2) to associate patient and disease characteristics with QST results. Methods: Ninety-one patients with painful CP and 28 healthy control participants completed a QST paradigm using static tests (muscle pressure stimulation and electrical skin stimulations) to unravel segmental and widespread hyperalgesia as a consequence of visceral pain. A dynamic conditioned pain modulation (CPM) paradigm was used as a proxy of pain modulation from the brainstem to inhibit incoming nociceptive barrage, and questionnaires were used to gather information on pain experience and quality of life. Results: Patients had impaired CPM compared with controls (18.0±29.3% vs. 30.9±29.3%, P=0.04) and were hypersensitive to pressure stimulation, specifically in the pancreatic (Th10) dermatome (P<0.001). The capacity of CPM was associated with clinical pain intensity (P=0.01) and (in the univariate analysis only) the use of opioids was associated with hyperalgesia to pressure stimulation (P<0.05). Conclusions: Sensitivity to pain in CP patients can be characterized by a simple bedside QST. Severe clinical pain in CP was associated with reduced CPM function and should be targeted in management.
Older Filipino immigrants’ reconfiguration of traditional filial expectations: a focus ethnographic study

Background: One of the many socio-cultural issues impacting older immigrants in host countries is the cultural expectations of filial piety from their adult children. Objective: To understand older Filipino immigrants’ beliefs and values towards filial expectations. Design: Focused ethnography. Results: Two major themes were identified. The first theme ‘moving away from filial expectations’ drew out older Filipino’s changing views of cultural expectations from their adult children. The second theme ‘maintaining cultural values through good family relationships’ highlighted the importance of acknowledging the cultural values considered to be most important by older Filipinos, which was having harmonious relationships and avoiding family conflict. Conclusion: The reconfigured expectation was salient with participants’ who identified ‘not being a burden’ to their adult children and the ardent desire to maintain positive family relationships. Impact Statement: Nurses need to be aware of changes to our current understanding of filial piety when providing care to older Filipinos.
Numerical analysis of frictional heat-stress coupled field at dynamic contact

A new analysis method was developed to simulate the dynamic process of a frictional heat-stress coupled field. The relationship between the frictional heat and the thermal stress was investigated for concave cylinder contact conditions. The results show that, as a nonlinear contact problem, the frictional heat at the contact areas changes with moving velocity in both value and distribution, and that the transient frictional heat at the dynamic condition has a peak within a cycle. The dynamic process of friction heat and thermal stresses affects diffusion of the frictional effects. The result can be helpful for dynamic simulation of diffusion lubrication of elements at elevated temperatures.
What are we targeting when we treat autism spectrum disorder? A systematic review of 406 clinical trials

The number of trials aimed at evaluating treatments for autism spectrum disorder has been increasing progressively. However, it is not clear which outcome measures should be used to assess their efficacy, especially for treatments which target core symptoms. The present review aimed to provide a comprehensive overview regarding the outcome measures used in clinical trials for people with autism spectrum disorder. We systematically searched the Web of KnowledgeSM database between 1980 and 2016 to identify published controlled trials investigating the efficacy of interventions in autism spectrum disorder. We included 406 trials in the final database, from which a total of 327 outcome measures were identified. Only seven scales were used in more than 5% of the studies, among which only three measured core symptoms (Autism Diagnostic Observation Schedule, Childhood Autism Rating Scale, and Social Responsiveness Scale). Of note, 69% of the tools were used in the literature only once. Our systematic review has shown that the evaluation of efficacy in intervention trials for autism spectrum disorder relies on heterogeneous and often non-specific tools for this condition. The fragmentation of tools may significantly hamper the comparisons between studies and thus the discovery of effective treatments for autism spectrum disorder. Greater consensus regarding the choice of these measures should be reached.
Endogenous Gastrin Collaborates With Mutant KRAS in Pancreatic Carcinogenesis.

OBJECTIVE The KRAS gene is the most frequently mutated gene in pancreatic cancer, and no successful anti-Ras therapy has been developed. Gastrin has been shown to stimulate pancreatic cancer in an autocrine fashion. We hypothesized that reactivation of the peptide gastrin collaborates with KRAS during pancreatic carcinogenesis. METHODS LSL-Kras; P48-Cre (KC) mutant KRAS transgenic mice were crossed with gastrin-KO (GKO) mice to develop GKO/KC mice. Pancreata were examined for 8 months for stage of pancreatic intraepithelial neoplasia lesions, inflammation, fibrosis, gastrin peptide, and microRNA expression. Pancreatic intraepithelial neoplasias from mice were collected by laser capture microdissection and subjected to reverse-phase protein microarray, for gastrin and protein kinases associated with signal transduction. RESULTS Elimination of gastrin in the KC mice significantly decreased KRAS, halted carcinogenesis, and resulted in marked decreased PanIN stage, inflammation, and fibrosis. Gastrin was not present in the normal mouse or human pancreas but became detectable as cancer developed. Reexpression of gastrin was mediated by miR-27a. Gastrin reexpression resulted in signal transduction by transactivation of tyrosine kinase receptors and activation of KRAS and mitogenic pathways that was reversed to the canonical signaling pathway in GKO/KC mice. Gastrin messenger RNA expression was analyzed in normal human pancreas tissues and compared with that of human pancreas cancer cells. CONCLUSIONS This study supports the mitogenic role of gastrin in activation of KRAS during pancreatic carcinogenesis.