Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics of Recent Aqua- and Orthoreovirus Isolates from Fish: Evolutionary Gain or Loss of FAST and Fiber Proteins and Taxonomic Implications

Family Reoviridae, subfamily Spinareovirinae, includes nine current genera. Two of these genera, Aquareovirus and Orthoreovirus, comprise members that are closely related and consistently share nine homologous proteins. Orthoreoviruses have 10 dsRNA genome segments and infect reptiles, birds, and mammals, whereas aquareoviruses have 11 dsRNA genome segments and infect fish. Recently, the first 10-segmented fish reovirus, piscine reovirus (PRV), has been identified and shown to be phylogenetically divergent from the 11-segmented viruses constituting genus Aquareovirus. We have recently extended results for PRV by showing that it does not encode a fusion-associated small transmembrane (FAST) protein, but does encode an outer-fiber protein containing a long N-terminal region of predicted α-helical coiled coil. Three recently characterized 11-segmented fish reoviruses, obtained from grass carp in China and sequenced in full, are also divergent from the viruses now constituting genus Aquareovirus, though not to the same extent as PRV. In the current study, we reexamined the sequences of these three recent isolates of grass carp reovirus (GCRV)–HZ08, GD108, and 104–for further clues to their evolution relative to other aqua- and orthoreoviruses. Structure-based fiber motifs in their encoded outer-fiber proteins were characterized, and other bioinformatics analyses provided evidence against the presence of a FAST protein among their encoded nonstructural proteins. Phylogenetic comparisons showed the combination of more distally branching, approved Aquareovirus and Orthoreovirus members, plus more basally branching isolates GCRV104, GCRV-HZ08/GD108, and PRV, constituting a larger, monophyletic taxon not suitably recognized by the current taxonomic hierarchy. Phylogenetics also suggested that the last common ancestor of all these viruses was a fiber-encoding, nonfusogenic virus and that the FAST protein family arose from at least two separate gain-of-function events. In addition, an apparent evolutionary correlation was found between the gain or loss of NS-FAST and outer-fiber proteins among more distally branching members of this taxon.
Coping Strategies and Benefit-finding in the Relationship between Non-disclosure and Depressive Symptoms among Breast Cancer Survivors in China.

OBJECTIVE Open communication about cancer diagnosis and relevant stress is frequently avoided among breast cancer survivors in China. Non-disclosure behavior may lead to negative psychological consequences. We aimed to examine the relationship between non-disclosure and depressive symptoms, and the role of coping strategies and benefit-finding in that relationship among Chinese breast cancer survivors. METHODS Using convenience sampling, we recruited 148 women in an early survivorship phase (up to 6 years post-treatment) in Nanjing, China. Participants were asked to complete a set of questionnaires in Chinese language, regarding sociodemographic characteristics, depressive symptoms, disclosure views, coping strategies, and benefit-finding. RESULTS A higher level of non-disclosure was associated with more depressive symptoms. This relationship was mediated by self-blame and moderated by benefit-finding. Specifically, non-disclosure was associated with depressive symptoms through self-blame. The impact of non-disclosure was minimized among the women with a higher level of benefit-finding. CONCLUSION Unexpressed cancer-related concern may increase self-blame, which leads to emotional distress among Chinese breast cancer survivors. Practicing benefit-finding may reduce the negative impact of non-disclosure. As a culturally appropriate way of disclosure, written expression may be beneficial to Chinese breast cancer patients.
Repeated Measurements of Cardiac Biomarkers in Atrial Fibrillation and Validation of the ABC Stroke Score Over Time

Background Cardiac biomarkers are independent risk markers in atrial fibrillation, and the novel biomarker–based ABC stroke score (age, biomarkers, and clinical history of prior stroke) was recently shown to improve the prediction of stroke risk in patients with atrial fibrillation. Our aim was to investigate the short‐term variability of the cardiac biomarkers and evaluate whether the ABC stroke risk score provides a stable short‐term risk estimate. Methods and Results According to the study protocol, samples were obtained at entry and also at 2 months in 4796 patients with atrial fibrillation followed for a median of 1.8 years in the ARISTOTLE (Apixaban for Reduction in Stroke and Other Thromboembolic Events in Atrial Fibrillation) trial. Cardiac troponin I, cardiac troponin T, and N‐terminal pro‐B‐type natriuretic peptide were measured with high‐sensitivity immunoassays. Associations with outcomes were evaluated by Cox regression. C indices and calibration plots were used to evaluate the ABC stroke score at 2 months. The average changes in biomarker levels during 2 months were small (median change cardiac troponin T +2.8%, troponin I +2.0%, and N‐terminal pro‐B‐type natriuretic peptide +13.5%) and within‐subject correlation was high (all ≥0.82). Repeated measurement of cardiac biomarkers provided some incremental prognostic value for mortality but not for stroke when combined with clinical risk factors and baseline levels of the biomarkers. Based on 8702 person‐years of follow‐up and 96 stroke/systemic embolic events, the ABC stroke score at 2 months achieved a similar C index of 0.70 (95% CI, 0.65–0.76) as compared with 0.70 (95% CI, 0.65–0.75) at baseline. The ABC stroke score remained well calibrated using predefined risk classes. Conclusions In patients with stable atrial fibrillation, the variability of the cardiac biomarkers and the biomarker‐based ABC stroke score during 2 months are small. The prognostic information by the ABC stroke score remains consistent and well calibrated with similar good predictive performance if patients are retested after 2 months. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT00412984.
Micro-CT as a Tool to Investigate the Efficacy of Tetramethylpyrazine in a Rat Spinal Cord Injury Model

Study Design. The micro-computed tomography (micro-CT) was applied to assess the effect of tetramethylpyrazine (TMP) on experimental spinal cord injury (SCI). Objective. The aim of the study was to explore the therapeutic effect of TMP on a rat SCI model using micro-CT. Summary of Background Data. SCI is a devastating event and always accompanied by severe vascular injury. Promoting angiogenesis after SCI has recently been recognized as a potential way to enhance the neurological function recovery. How the TMP promotes angiogenesis and improved locomotor function recovery after SCI has, however, not been fully clarified. In this study, we used micro-CT to evaluate the effect on the microvasculature changes after TMP treatment. Methods. The contusion SCI model was induced in rats by a modified Allen's impact method. In the TMP treatment group, rats were injected intraperitoneally with TMP. The control group was treated with saline. Hindlimb motor function was evaluated using the Basso, Beattie, Bresnahan score. Histology was employed to examine the pathological changes and quantified at 28 days after injury. Spinal cord vessel network and angiogenesis were assessed using micro-CT. Results. Angiogenesis was increased in groups treated with TMP compared with rat in the control groups (P < 0.05). Micro-CT vividly depicted the three-dimensional morphology changes of the spinal cord microvasculature after injury and demonstrated more vessels number, vessel volume fraction, and vessel connectivity value in the groups treated with TMP than in the control groups (P < 0.05). In addition, the injury-induced lesion area in TMP group was attenuated in comparison with control groups. Similarly, neurological functions were greatly improved in groups treated with TMP compared with rats in the control groups. Conclusion. Micro-CT is useful for detecting angiogenesis after SCI. TMP therapy reduced the neuronal loss, promoted angiogenesis, and exerted a positive effect on neurological function recovery after SCI. Level of Evidence: N/A
2D Aeroacoustic Analysis of Flow in the Flame Trench

We present here a methodology for using the commercial software ANSYSFLUENT to predict the acoustic field associated with Space-Launch System (SLS). We consider a two-dimensional model of flame deflector, and flame trench. The ANYSYS code is then used to simulate the internal flow. Both the steady state case is considered along with two other cases where the inflow has a harmonic component. A FfowcsWilliams Hawking (FWH) surface is then constructed within the computational domain to use the computed flow fluctuations to obtain the acoustic field. The acoustic data was then compared to the experimental data. When using the ANSYS code for this flow situation, the residuals did not converge but reached an asymptotic oscillatory state. The fluctuation in the residual is too large to consider the computed flow fluctuations to be the sound source. Therefore, the results should be interpreted with caution as a first-attempt preliminary results. However, the calculated sound field qualitatively resembles the experimental observations. This may support the need to address the conversion issue and the need to extend the approach to the realistic three-dimensional case.
Sensitivity of the Breastfeeding Motivational Measurement Scale: A Known Group Analysis of First Time Mothers

Breastfeeding has immense public health value for mothers, babies, and society. But there is an undesirably large gap between the number of new mothers who undertake and persist in breastfeeding compared to what would be a preferred level of accomplishment. This gap is a reflection of the many obstacles, both physical and psychological, that confront new mothers. Previous research has illuminated many of these concerns, but research on this problem is limited in part by the unavailability of a research instrument that can measure the key differences between first-time mothers and experienced mothers, with regard to the challenges they face when breastfeeding and the instructional advice they require. An instrument was designed to measure motivational complexity associated with sustained breast feeding behaviour; the Breastfeeding Motivational Measurement Scale. It contains 51 self-report items (7 point Likert scale) that cluster into four categories related to perceived value of breast-feeding, confidence to succeed, factors that influence success or failure, and strength of intentions, or goal. However, this scale has not been validated in terms of its sensitivity to profile the motivation of new mothers and experienced mothers. This issue was investigated by having 202 breastfeeding mothers (100 first time mothers) fill out the scale. The analysis reported in this paper is a three factor solution consisting of value, midwife support, and expectancies for success that explained the characteristics of first time mothers as a known group. These results support the validity of the BMM scale as a diagnostic tool for research on first time mothers who are learning to breastfeed. Further research studies are required to further test the validity of the scale in additional subgroups.
Intravesical BCG Induces CD4+ T-Cell Expansion in an Immune Competent Model of Bladder Cancer

Intravesical bacillus Calmette–Guéerin (BCG) instillations are standard of care for early stage bladder cancer. BCG was found to recruit T cells to the bladder, but their phenotype was unchanged, implying that combining T cell–activating agents with BCG might improve clinical activity. Intravesical bacillus Calmette–Guérin (BCG) immunotherapy is the standard of care in treating non–muscle-invasive bladder cancer, yet its mechanism of action remains elusive. Both innate and adaptive immune responses have been implicated in BCG activity. Although prior research has indirectly demonstrated the importance of T cells and shown a rise in CD4+ T cells in bladder tissue after BCG, T-cell subpopulations have not been fully characterized. We investigated the relationship between effector and regulatory T cells in an immune competent, clinically relevant rodent model of bladder cancer. Our data demonstrate that cancer progression in the N-methyl-N-nitrosourea (MNU) rat model of bladder cancer was characterized by a decline in the CD8/FoxP3 ratio, consistent with decreased adaptive immunity. In contrast, treatment with intravesical BCG led to a large, transient rise in the CD4+ T-cell population in the urothelium and was both more effective and immunogenic compared with intravesical chemotherapy. Whole-transcriptome expression profiling of posttreatment intravesical CD4+ and CD8+ T cells revealed minimal differences in gene expression after BCG treatment. Together, our results suggest that although BCG induces T-cell recruitment to the bladder, the T-cell phenotype does not markedly change, implying that combining T-cell–activating agents with BCG might improve clinical activity. Cancer Immunol Res; 5(7); 594–603. ©2017 AACR.
Rural Residents’ Perspectives on Multiple Morbidity Management and Disease Prevention

Middle-aged and older adults often experience several simultaneously occurring chronic conditions or “multiple morbidity” (MM). The task of both managing MM and preventing chronic conditions can be overwhelming, particularly in populations with high disease burdens, low socioeconomic status, and health care provider shortages. This article sought to understand Appalachian residents’ perspectives on MM management and prevention. Forty-one rural Appalachian residents aged 50 and above with MM were interviewed about disease management and colorectal cancer (CRC) prevention. Transcripts were examined for overall analytic categories and coded using techniques to enhance transferability and rigor. Participants indicate facing various challenges to prevention due, in part, to conditions within their rural environment. Patients and providers spend significant time and energy on MM management, often precluding prevention activities. This article discusses implications of MM management for CRC prevention and strategies to increase disease prevention among this rural, vulnerable population burdened by MM.
An image fusion study of the geometric accuracy of magnetic resonance imaging with the Leksell stereotactic localization system1

A special acrylic phantom designed for both magnetic resonance imaging (MRI) and computed tomography (CT) was used to assess the geometric accuracy of MRI‐based stereotactic localization with the Leksell stereotactic head frame and localizer system. The acrylic phantom was constructed in the shape of a cube, 164 mm in each dimension, with three perpendicular arrays of solid acrylic rods, 5 mm in diameter and spaced 30 mm apart within the phantom. Images from two MR scanners and a CT scanner were obtained with the same Leksell head frame placement. Using image fusion provided by the Leksell GammaPlan (LGP) software, the coordinates of the intraphantom rod positions from two MRI scanners were compared to that of CT imaging. The geometric accuracy of MR images from the Siemens scanner was greatly improved after the implementation of a special software patch provided by the manufacturer. In general, much better accuracy was achieved in the transverse plane where images were acquired. Most distortion was found around the periphery while least distortion was present in the middle and most other parts of the phantom. For most intracranial lesions undergoing stereotactic radiosurgery, accuracy of target localization can be achieved within size of a voxel, especially with the Siemens scanner. However, extra caution should be taken for imaging of peripheral lesions where the distortion is the greatest. PACS number(s): 87.61. –c, 87.57. –s
Design, manufacturing and optimization of PM-SMC motors

Soft magnetic composite (SMC), as a relatively new magnetic material, has attracted much attention in the design of electrical machines. This paper aims to discuss the specific and common problems in the design of permanent magnet (PM) motors with SMC cores. Firstly, the motor topology design is introduced for taking advantage of the SMC properties. Then, precise material testing and modeling methods are presented for the accurate core loss calculation of PM-SMC motors. Considering the influence of manufacturing process, two design optimization approaches are utilized for enhancing the motor performance. For improving the electromagnetic properties of the SMC cores, the orthogonal experiment is proposed for investigating and optimizing the heat treatment process. Considering the manufacturing tolerances in the actual production, the robust tolerance design optimization approach is introduced for pursuing the optimal motor performance and manufacturing cost with high reliability.
ABCB1 1199G>A polymorphism (rs2229109) affects the transport of imatinib, nilotinib and dasatinib.

AIM ABCB1 (or P-glycoprotein) is implicated in the multidrug-resistance phenotype, including the resistance toward anticancer drugs such as tyrosine kinase inhibitors (TKIs). The purpose of this study was to evaluate in vitro the influence of the ABCB1 1199G>A SNP on ABCB1 transport activity toward selected TKIs (imatinib, nilotinib and dasatinib) that are currently used in chronic myelogenous leukemia. MATERIAL & METHODS Two different cell lines, HEK293 and K562, were stably transfected with ABCB1 1199G wild-type or ABCB1 1199A variant allele. The impact of this polymorphism on accumulation and antiproliferative effects of imatinib, nilotinib and dasatinib was evaluated. RESULTS In K562 models, the expression of Asn400 variant protein was associated with lower antiproliferative effects of imatinib, nilotinib and dasatinib compared with Ser400 wild-type protein. Moreover, in HEK293 cells, imatinib and nilotinib intracellular accumulation were lower in variant compared with wild-type models. CONCLUSION Imatinib, nilotinib and dasatinib are transported more efficiently by the ABCB1 variant (Asn400) compared with the wild-type (Ser400) protein. The impact of ABCB1 1199G>A SNP on TKI response should be further investigated in chronic myelogenous leukemia patients.
Junctioning longitudinally adjacent PTVs with Helical TomoTherapy

Irradiation of longitudinally adjacent PTVs with Helical TomoTherapy (HT) may be clinically necessary, for example in treating a recurrent PTV adjacent to a previously‐treated volume. In this work, the parameters which influence the cumulative dose distribution resulting from treating longitudinally adjacent PTVs are examined, including field width, pitch, and PTV location. In‐phantom dose distributions were calculated for various on‐ and off‐axis cylindrical PTVs and were verified by ion chamber and film measurement. Dose distributions were calculated to cover 95% of the PTV by the prescribed dose (DP) using 25 and 50 mm long HT fields with pitches of either 0.3 or 0.45. These dose distributions where then used to calculate the 3D dose distribution in the junction region between two PTVs. The best junction uniformity was obtained for fields of equal width, with larger fields providing better intra‐PTV dose homogeneity than smaller fields. Junctioning fields of different widths resulted in a much larger dose inhomogeneity, but this could be improved significantly by dividing the junction end of the PTV treated with the smaller field into multiple (up to 4) sub‐PTVs, with the prescribed dose in each sub‐PTV decreasing with proximity to the junction region. This provided a PTV matching with dose homogeneity similar to that achieved when junctioning two PTVs, both irradiated by the 50 mm field, and provided a distribution where 95% of the PTV received at least the prescribed dose, with maximum excursions from prescribed dose varying from −19% to +13%. We conclude that junctioning adjacent PTVs is possible. Treating longitudinally adjacent PTVs with different widths is a challenge, but dose uniformity is improved by breaking PTVs into multiple contiguous sub‐PTVs modified to feather (broaden) the effective junctioning region. PACS number: 87.55. D
Animal Models of Zika Virus Infection, Pathogenesis, and Immunity

ABSTRACT Zika virus (ZIKV) is an emerging mosquito-transmitted flavivirus that now causes epidemics affecting millions of people on multiple continents. The virus has received global attention because of some of its unusual epidemiological and clinical features, including persistent infection in the male reproductive tract and sexual transmission, an ability to cross the placenta during pregnancy and infect the developing fetus to cause congenital malformations, and its association with Guillain-Barré syndrome in adults. This past year has witnessed an intensive effort by the global scientific community to understand the biology of ZIKV and to develop pathogenesis models for the rapid testing of possible countermeasures. Here, we review the recent advances in and utility and limitations of newly developed mouse and nonhuman primate models of ZIKV infection and pathogenesis.
Revealing nascent proteomics in signaling pathways and cell differentiation

Significance Deciphering which networks of genes allow cells to rapidly respond to environmental cues is key to understanding processes such as proliferation, differentiation, and death. Here, we describe a technique to quantitatively identify nascent protein synthesis using O-propargyl-puromycin (OPP), a specific covalent label of growing polypeptides, which are then isolated and measured by mass spectrometry. This technique, named OPP-mediated identification (OPP-ID), is applicable across a wide array of cell types for identification of proteins in situ. We illustrate the capability of OPP-ID by identifying a constellation of mammalian target of rapamycin (mTOR)-dependent gene networks and uncovering an array of genes involved in early erythroid progenitor expansion. OPP-ID is a powerful technique to study how cells modulate nascent protein expression to respond to stresses and stimuli. Regulation of gene expression at the level of protein synthesis is a crucial element in driving how the genetic landscape is expressed. However, we are still limited in technologies that can quantitatively capture the immediate proteomic changes that allow cells to respond to specific stimuli. Here, we present a method to capture and identify nascent proteomes in situ across different cell types without disturbing normal growth conditions, using O-propargyl-puromycin (OPP). Cell-permeable OPP rapidly labels nascent elongating polypeptides, which are subsequently conjugated to biotin-azide, using click chemistry, and captured with streptavidin beads, followed by digestion and analysis, using liquid chromatography–tandem mass spectrometry. Our technique of OPP-mediated identification (OPP-ID) allows detection of widespread proteomic changes within a short 2-hour pulse of OPP. We illustrate our technique by recapitulating alterations of proteomic networks induced by a potent mammalian target of rapamycin inhibitor, MLN128. In addition, by employing OPP-ID, we identify more than 2,100 proteins and uncover distinct protein networks underlying early erythroid progenitor and differentiation states not amenable to alternative approaches such as amino acid analog labeling. We present OPP-ID as a method to quantitatively identify nascent proteomes across an array of biological contexts while preserving the subtleties directing signaling in the native cellular environment.