Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional and Biochemical Characterization of Hepatitis C Virus (HCV) Particles Produced in a Humanized Liver Mouse Model*

Background: We compared viral subpopulations derived from humanized liver mouse model versus cell culture. Results: In vivo and in vitro produced particles show different biophysical properties and receptor usage. Conclusion: In vivo models allow functional investigations on how lipid metabolism and hepatic environment influence HCV entry. Significance: HCV produced from humanized liver mice may better reflect the characteristics of virus from HCV-infected patients. Lipoprotein components are crucial factors for hepatitis C virus (HCV) assembly and entry. As hepatoma cells producing cell culture-derived HCV (HCVcc) particles are impaired in some aspects of lipoprotein metabolism, it is of upmost interest to biochemically and functionally characterize the in vivo produced viral particles, particularly regarding how lipoprotein components modulate HCV entry by lipid transfer receptors such as scavenger receptor BI (SR-BI). Sera from HCVcc-infected liver humanized FRG mice were separated by density gradients. Viral subpopulations, termed HCVfrg particles, were characterized for their physical properties, apolipoprotein association, and infectivity. We demonstrate that, in contrast to the widely spread distribution of apolipoproteins across the different HCVcc subpopulations, the most infectious HCVfrg particles are highly enriched in apoE, suggesting that such apolipoprotein enrichment plays a role for entry of in vivo derived infectious particles likely via usage of apolipoprotein receptors. Consistent with this salient feature, we further reveal previously undefined functionalities of SR-BI in promoting entry of in vivo produced HCV. First, unlike HCVcc, SR-BI is a particularly limiting factor for entry of HCVfrg subpopulations of very low density. Second, HCVfrg entry involves SR-BI lipid transfer activity but not its capacity to bind to the viral glycoprotein E2. In conclusion, we demonstrate that composition and biophysical properties of the different subpopulations of in vivo produced HCVfrg particles modulate their levels of infectivity and receptor usage, hereby featuring divergences with in vitro produced HCVcc particles and highlighting the powerfulness of this in vivo model for the functional study of the interplay between HCV and liver components.
Microencapsulation by spray drying of lemon essential oil: Evaluation of mixtures of mesquite gum–nopal mucilage as new wall materials

Abstract Mesquite gum (MG) and nopal mucilage (NM) mixtures were used for microencapsulation of lemon essential oil (LEO) by spray drying. Emulsions of MG, NM and MG–NM mixtures (25–75, 50–50, 75–25) were evaluated according to the droplet size (1.49–9.16 μm), viscosity and zeta potential (−16.07 to −20.13 mV), and microcapsules were characterised in particle size (11.9–44.4 μm), morphology, volatile oil retention (VOR) (45.9–74.4%), encapsulation efficiency (EE) (70.9–90.6%), oxidative stability and thermal analysis. The higher concentration of MG led to smaller droplet sizes and lower viscosity in the emulsions, and smaller particle sizes with the highest VOR in microcapsules. The higher concentration of NM induced to higher viscosity in the emulsions, and larger particle sizes with the highest values of EE and oxidative stability in microcapsules. This work shows evidence that MG–NM mixtures can have synergic effect in desirable characteristics such as retention and shelf life extension of LEO in microcapsules.
#A11 INTEGERS 14 (2014) ABELIAN COMPLEXITY OF FIXED POINT OF MORPHISM

We study the combinatorics of vtm, a variant of the Thue-Morse word generated by the non-uniform morphism 0 7! 012, 1 7! 02, 2 7! 1 starting with 0. This infinite ternary sequence appears a lot in the literature and finds applications in several fields such as combinatorics on words; for example, in pattern avoidance it is often used to construct infinite words avoiding given patterns. It has been shown that the factor complexity of vtm, i.e., the number of factors of length n, is ⇥(n); in fact, it is bounded by 10 3 n for all n, and it reaches that bound precisely when n can be written as 3 times a power of 2. In this paper, we show that the abelian complexity of vtm, i.e., the number of Parikh vectors of length n, is O (log n) with constant approaching 4 (assuming base 2 logarithm), and it is ⌦ (1) with constant 3 (and these are the best possible bounds). We also prove some results regarding factor indices in vtm. 1F. Blanchet-Sadri and Nathan Fox’s research was supported by the National Science Foundation under Grant No. DMS–1060775. 2James D. Currie and Narad Rampersad’s research was supported by NSERC Discovery grants. INTEGERS: 14 (2014) 2
Latchup performance of retrograde and conventional n-well CMOS technologies

The static and transient latchup performance of conventional and retrograde n-well CMOS technologies is compared. The retrograde n-well structures are shown to have superior latchup immunity, due primarily to the reduced n-well sheet resistance and the greater tolerance to thin p on p+epitaxial material.
The association of Chlamydia trachomatis and Mycoplasma genitalium with non-gonococcal urethritis: observations on heterosexual men and their female partners

Our objectives were to study the distribution of Chlamydia trachomatis and Mycoplasma genitalium in men with or without non-gonococcal urethritis (NGU) and their respective female partners. A case-control study was carried out to which men with or without NGU and their female partners were recruited. All study participants were tested for the presence of C. trachomatis and M. genitalium. An analysis firstly of the distribution of each of these microorganisms among men with or without urethritis and their respective female partners was carried out. Furthermore, we examined the association of each of these microorganisms and NGU when the other had been excluded. Chlamydia trachomatis was present in 14 (36%) of 39 men with NGU compared to none of 12 men without NGU (P = 0.022). The prevalence rates for female partners of men with NGU were 10 (26%) of 39 compared to none of 12 partners of men without NGU (P = 0.092). M. genitalium was detected in 12 (33%) of 36 men with NGU compared to 1 (9%) of men without NGU (not significant; P = 0.147). The prevalence rates for female partners of men with NGU were 10 (32%) of 31 women compared to none of 7 partners of men without NGU (not significant; P = 0.156). There was a greater concordance than discordance of carriage of each of the 2 microorganisms among the study couples and each tended to be carried independently of the other by men. Analysis of the association between the presence of C. trachomatis in men and NGU was significantly improved by the exclusion of men with M. genitalium (P = 0.0058). Likewise, the association between the presence of M. genitalium in men and NGU was significantly improved by the exclusion of couples in whom either the man or woman was C. trachomatis-positive (P = 0.049). The independent carriage of C. trachomatis and M. genitalium by men with NGU, coupled with the improved association between each pathogen and NGU by exclusion of the other provides support for the separate role of each in the aetiology of NGU.
Influence of water absorption on plastic optical fibers.

The influence of absorbed water on the attenuation loss of plastic optical fibers (POFs) is discussed. By lowering the POF loss, absorbed water becomes the significant constituent for the loss of POFs. The degree of loss increment due to water absorption depends on the relative humidity of the environment where the POFs exist. A low-loss deuterated PMMA core POF is thought to be suitable for use as a visible-wavelength-region optical signal transmission medium. A deuterated polystyrene core POF can be used as a near-IR transmission medium.
Sleep telemedicine: patient satisfaction and treatment adherence.

OBJECTIVE Obstructive sleep apnea is common, but access to diagnosis remains limited. Telemedicine may allow greater access to care; however, its effect on patient satisfaction and treatment adherence is unknown. This study compares patient satisfaction and continuous positive airway pressure (CPAP) adherence of patients seen by videoconference with those seen in person. MATERIALS AND METHODS New patients seen via video or in person at a sleep center completed a survey, with three questions pertaining to satisfaction with the provider. Questions were scored 1-5; the sum was the patient satisfaction score. CPAP adherence was retrospectively analyzed in patients who met the physician via video or in person. Percentage of nights CPAP was used for ≥4 h and average minutes of CPAP use per night over 2 consecutive weeks were compared. RESULTS A Mann-Whitney test compared patient satisfaction of the 90 subjects (of whom, 56 met physician in person and 34 via video). Mean scores (in person, 14.82; video, 14.91; p=0.851) did not differ between groups. Mann-Whitney tests compared CPAP adherence in the 172 subjects (of whom, 111 met physician in person and 61 via video). Mean percentage of nights CPAP was used ≥4 h (in person, 71%; video, 65%; p=0.198) and the average minutes per night of CPAP use (in person, 340.55; video, 305.31; p=0.153) did not differ between groups. CONCLUSIONS The findings indicate that patients were equally satisfied with their provider and adherent to CPAP treatment whether they were seen in person or via video. Videoconferencing may improve access to patient care without reducing patient satisfaction or treatment adherence.
Apoptosis in the immune system: 1. Fas‐induced apoptosis in monocytes‐derived human dendritic cells

Dendritic cells (DC) are cells of the hematopoietic system specialized in capturing antigens and initiating T cell‐mediated immune responses. We show here that human DC generated from adherent peripheral blood mononuclear cells (PBMC) after in vitro stimulation with granulocyte macrophage colony stimulating factor (GM‐CSF) and interleukin‐4 (IL‐4) express Fas antigen (APO‐1, CD95) and can undergo apoptosis upon triggering of Fas by monoclonal antibodies. Immature monocytes‐derived dendritic cells (MDDC) upregulate CD86 and HLA‐DR expression and develop dendrites and veiled processes. Flow cytometry analysis revealed CD95 expression in approx. 40% of these MDDC and incubation with anti‐CD95 mAb (0.5μg/ml) induced apoptosis when compared to untreated controls. The extent of apoptosis induced by the agonist anti‐Fas antibody strongly related to the percentage of cells expressing CD 95. Upon tumor necrosis factor α (TNF‐α) additional stimulation, MDDC assumed a characteristic mature dendritic cells morphology showing prolonged veils, CD83 expression, and high levels of HLA‐DR. These cells have downregulated their Fas receptors (to approx. 20%) and undergo apoptosis to a lesser extent when treated with anti‐CD 95, as demonstrated by the hardly noticeable effect of this antibody on the viability of cultured cells as compared to controls. Thus, upon TNF‐α induced maturation, MDDC became resistant to Fas‐induced apoptosis. The apoptotic episodes surrounding the earlier stage of DC differentiation appeared to be mediated by Fas. In contrast, a Fas independent pathway is probably responsible for the apoptotic events associated with terminally differentiated DC.
Endocrine-Related Cancer ( 2007 ) 14 43 – 60 p 53 family proteins in thyroid cancer

At variance with other human malignancies, p53 mutations are not frequent in thyroid cancer and are believed to be responsible mainly for cancer progression to poorly differentiated and aggressive phenotype. p63 and p73, two proteins with a high degree of homology with p53, are overexpressed in thyroid cancer, but their role in cancer initiation or progression is controversial. Regulation of p53 family protein function depends on: (1) the balance between the expression of transcriptionally active (p53, TAp63, and TAp73) and inactive isoforms (DNp63 and DNp73); (2) their interaction and competition at DNA-responsive elements; (3) their interaction with regulatory proteins, either inhibitory or activating. In thyroid cancer, therefore, although mutations of the p53 oncosuppressor protein family are rare, other mechanisms are present, including aberrant expression of p53 family dominant negative isoforms, up-regulation of inhibitory proteins, and functional inhibition of activating proteins. The overall result is a defective oncosuppressor activity. These inactivating mechanisms may be present in the early stages of thyroid cancer and in different cancer histotypes. A better understanding of this complex network may not only ameliorate our comprehension of cancer biology, but also open the possibility of innovative diagnostic procedures and the development of targeted therapies. Endocrine-Related Cancer (2007) 14 43–60 p53 in thyroid cancer Oncogene gain of function is the most frequent molecular alteration described in thyroid cancer. It mainly includes the aberrant activation of the RAS/RAF/MEK/ERK pathway (Kroll 2004, Hunt 2005). These alterations regard the rearrangements of Ret/PTC and Trk tyrosine kinase receptors and point mutations of RAS or BRAF genes (Kroll 2004, Hunt 2005). Recently, mutations in the PI3KCA gene, resulting from the constitutive activation of the PI-3K pathway, have also been described in anaplastic thyroid carcinomas (Garcia-Rostan et al. 2005). Loss of function of tumor suppressor proteins may also occur in thyroid cancer and includes PAX-8/PPARg rearrangement, PTEN down-regulation, b-catenin, and p53 mutations (Kroll 2004, Hunt 2005). While inactivating mutations of the p53 gene is very frequent in human cancers (50% of all human malignancies), they have been found in only 10% of thyroid carcinomas (Olivier et al. 2002; Fig. 1A) and mainly in poorly differentiated and aggressive histotypes. These observations and the indolent progression of most thyroid carcinomas have brought Endocrine-Related Cancer (2007) 14 43–6
High-speed apolipoprotein E genotyping and apolipoprotein B3500 mutation detection using real-time fluorescence PCR and melting curves.

Apolipoproteins play a central role in cholesterol transport by their association to lipoproteins and their function as ligands for receptors, cofactors, or structural proteins. Mutations and polymorphisms in a variety of apolipoproteins lead to lipoprotein metabolism disorders and/or susceptibility to cardiovascular disease. In familial defective apolipoprotein B-100, the clearance of LDL particles from the circulation is impaired because of reduced affinity of the apolipoprotein (apo) B component of LDL for the LDL receptor as a result of a G-to-A mutation at nucleotide 10708 in exon 26 of the apoB gene, which causes substitution of Arg3500 for Gln (1)(2). The frequency of the mutation is 1 in 700 in the general population (3). Heterozygous individuals have increased serum concentrations of cholesterol. Apolipoprotein E (apoE) likewise is involved in the clearance of HDL, contributing to reverse cholesterol transport (4). Genetic variation at the APOE locus in humans is an important determinant of plasma lipid concentrations and relative risk of atherosclerosis (5). Among several rare variants, three major alleles have been identified in the population: E2 , E3 , and E4 . The most common E3 isoform is distinguished by cysteine at position 112 and arginine at position 158 in the receptor-binding region of apoE. The E4 isoform (Arg112 and Arg158) is associated with increased cholesterol, thus enhancing the risk of heart disease (5). In addition, E4 / E4 individuals have a very high risk for developing Alzheimer disease(6). Most patients with type III hyperlipidemia are homozygous for the E2 allele (Cys112 and Cys158). To date, genotyping for apoE is mainly performed by PCR, followed by digestion with restriction enzymes and restriction fragment length polymorphism (RFLP) analysis, and separation of the resulting DNA fragments on agarose or acrylamide gels (7). For apoB3500, an allele-specific …
Effects of leukocyte-platelet rich fibrin on postoperative complications of direct sinus lifting.

BACKGROUND Blood products have been widely used in soft tissue and bone regeneration in oral and maxillofacial surgery. The purpose of this study is to evaluate the effects of leukocyte-platelet rich fibrin (L-PRF) following direct sinus lifting procedure. METHODS Twenty-eight patients were included in the study. Direct sinus lifting was performed via lateral window approach under conscious sedation and local anesthesia. Bony window and sinus floor elevation were performed using piezosurgery device. Two groups were formed. In the first group an allogenous bone graft and L-PRF mixture was used as grafting material. The L-PRF membrane was used to close the lateral window. In the second group, only allogenous bone was used for grafting and resorbable collagen membrane was used to close the lateral window. Pain, swelling, sleeping, eating, phonetics, activities of daily living, missed work days and soft tissue healing were evaluated postoperatively. RESULTS Data of 24 patients were evaluated. Improvements were seen in the studied parameters in the L-PRF group; however, the difference was not significant between the two groups (P>0.05). CONCLUSIONS The use of L-PRF and allogenous bone graft in combination with L-PRF membrane does not significantly improve postoperative complications following direct sinus lifting.
Extraction and partial purification of the histamine-sensitizing factor of Bordetella pertussis.

The histamine-sensitizing factor (HSF) of Bordetella pertussis has been recovered in soluble form by treatment of bacterial cells with 4 M urea, 1 M NaCl buffered with 0.1 M sodium phosphate at pH 6.4. Besides histamine-sensitizing activity, this extract has leukocytosis-promoting activity and is a potent adjuvant for hemagglutinating and reaginic antibodies. Through extraction and gel filtration column chromatography, a 280-fold purification of HSF has been achieved resulting in a purified preparation with a 50% sensitizing dose (SD50) of about 60 ng. Chemical analysis of this purified extract demonstrated protein and lipid to be the major components. Since other pertussis biologic activity such as leukocytosis-promoting and adjuvant activities in addition to histamine-sensitizing activity were still present in this highly purified extract of HSF, it is possible that one molecular species might be responsible for all these activities.
Fast Forward Rounds: An Effective Method for Teaching Medical Students to Transition Patients Safely Across Care Settings

Adverse events commonly occur during hospital‐to‐home transitions and cause substantial morbidity. This study evaluated the effectiveness of Fast Forward Rounds (FFR), a novel educational intervention that aims to foster awareness of the essential elements of transitional care in 3rd‐year medical students. FFR consists of two 90‐minute sessions using lectures, an interactive video, small‐group discussion, and a team‐based learning exercise. It emphasizes functional assessment to identify patients at risk for poor discharge outcomes, promotes interdisciplinary collaboration to link vulnerable patients with appropriate services, reviews Medicare and Medicaid reimbursement, and teaches development of comprehensive care plans. Using a pre/posttest design, participants' knowledge, attitudes and behaviors within the domains of transitional care, functional assessment, interdisciplinary team, community resources, and reimbursement were assessed. Of 103 students, 99.0% attended Session 1 and 97.1% attended Session 2 (pretest completion rate 99.0%, posttest 94.1%). Significant improvements were found in all domains, with the largest gains seen in transitional care. After the intervention, 56.0% identified medication errors as the most common source of adverse events after discharge (vs 14.9% before the intervention, P<.001). Significantly more participants reported feeling competent or expert in safely discharging chronically ill patients (66.3% vs 9.8%, P<.001) and in educating patients about discharge medications (75.8% vs 28.4%, P<.001). Participants also reported changes in transitional care behaviors (e.g., 71.6% now review the discharge medication list with patients and caregivers ≥50% of the time (vs 42.3%, P=.002)). A multimodal educational intervention for medical students increased their transitional care knowledge, reported frequency of transitional care behaviors, and perceived competence in managing the discharge process.
Efficiency and Mechanism of Antigen-specific CD8+ T-cell Activation Using Synthetic Long Peptides

Synthetic long peptides that contain immunogenic T-cell epitopes have been used to induce activation of antigen-specific CD8+ T cells in vitro for immune monitoring or adoptive transfer, or in vivo after peptide vaccination. However, the efficiency and mechanisms of presentation of exogenous long peptides in human leukocyte antigen (HLA) class I remain to be elucidated. In this study, we demonstrated that the efficiency of antigen-specific CD8+ T-cell activation using extended peptide variants of common viral epitopes is variable. We demonstrated that processing and HLA class I presentation of the long peptides were not dependent on the proteasome and transporter associated with antigen processing, illustrating that the classic route of HLA class I presentation was not required for activation of specific CD8+ T cells by exogenous synthetic long peptides. Although long peptides were shown to bind to the relevant HLA class I molecules, peptide trimming was likely to be essential for optimal HLA class I presentation and T-cell activation. As the proteasome was not required for processing of exogenous peptides, it is very likely that peptide trimming was mediated by peptidases, which may be located extracellularly at the cell surface, in the cytosol, endoplasmic reticulum, or in endosomal and lysosomal compartments. Furthermore, the results suggested that processing of the correct minimal peptides was facilitated by binding in HLA class I molecules. This mechanism of HLA-guided processing may be important in HLA class I presentation of exogenous long peptides to induce activation of specific CD8+ T cells.
Vertebral artery injury during anterior cervical vertebral surgery caused by transverse foramen malformation-appendix : case report and literature review

One male patient at 59 years old of age was diagnosed as cervical myelopathy for unsteady gait and stiff lower limbs, followed by cervical 3/4 and 5/6 discectomy plus bone grafting and internal fixation, when processing the superior endplate of left cervical 4 disk, a large number of arterial bleeding occurred, which was stopped by packing method, and followed by continued cervical discectomy plus internal fixation. This patient was followed up for five years, the left vertebral artery was blocked, while no significant vascular injury-associated complication occurred, nor the symptoms of spinal cord further aggravated. We believed that the missed-diagnosed transverse foramen malformation before surgery led to the occurrence of almost catastrophic intraoperative bleeding, which might be ignored by the vast majority of clinicians and imaging physicians in preoperative routine magnetic resonance imaging (MRI) examination, therefore, paying high attention to this situation, as well as preoperative vertebral CT scanning or vertebral artery angiography would be essential.