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https://www.readbyqxmd.com/read/28645144/increased-alignment-sensitivity-improves-the-usage-of-genome-alignments-for-comparative-gene-annotation
#1
Virag Sharma, Michael Hiller
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28644991/glimpses-into-the-blind-spot-social-interaction-and-autism
#2
REVIEW
Kristen Bottema-Beutel
A primary feature of autism spectrum disorder (ASD) is marked difficulty in social interactions. Despite the centrality of social interaction differences to the clinical presentation of ASD, only a small portion of research in this field characterizes interaction in everyday social contexts. This theoretical paper reviews the growing corpus of interactional research on ASD, including discourse analysis (DA) and conversation analysis (CA) approaches. DA and CA are micro-analytic methods aimed at understanding the organizational structure of, and actions pursued within, social encounters...
June 16, 2017: Journal of Communication Disorders
https://www.readbyqxmd.com/read/28644798/joint-alignment-of-multiple-point-sets-with-batch-and-incremental-expectation-maximization
#3
Dimitrios Georgios Evangelidis, Radu Horaud
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model set and a data set. The main drawback of this strategy is that the model set may contain noise and outliers, which negatively affects the estimation of the registration parameters. In contrast, the proposed formulation treats all the point sets on an equal footing. Indeed, all the points are drawn from a central Gaussian mixture, hence the registration is cast into a clustering problem...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28644782/how-should-resident-physicians-respond-to-patients-discomfort-and-students-moral-distress-when-learning-procedures-in-academic-medical-settings
#4
Bonnie M Miller
In this scenario, a medical student, Lauren, experiences moral distress because she feels that learning to perform a procedure on a patient who requested not to be used for "practice" puts her own interests above the patient's. Lauren might also worry that the resident physician is misrepresenting her abilities. The resident physician could help alleviate Lauren's distress and align her interests with the patient's by more clearly explaining the training situation to the patient and seeking the patient's approval...
June 1, 2017: AMA Journal of Ethics
https://www.readbyqxmd.com/read/28644625/chemically-modified-surface-having-a-dual-structured-hierarchical-topography-for-controlled-cell-growth
#5
Lun Peng, Shenglin Zhou, Bo Yang, Meimei Bao, Gaojian Chen, Xiaohua Zhang
This report describes a technique for fabricating dual-structured hierarchical surface topography on the surface of polydimethylsiloxane (PDMS) films through simply replicating prefabricated patterns and wrinkling PDMS films. To enhance the biocompatibility of PDMS films we synthesize a biocompatible dopamine-glycopolymer, which is utilized to modify the chemical feature of the PDMS surface. Dopamine component in this copolymer is introduced for the formation of a carbohydrate layer on the surface of PDMS films due to its excellent adhesion...
June 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28644492/electronic-properties-of-blue-phosphorene-graphene-and-blue-phosphorene-graphene-like-gallium-nitride-heterostructures
#6
Minglei Sun, Jyh-Pin Chou, Jin Yu, Wencheng Tang
Blue phosphorene (BlueP) is a graphene-like phosphorus nanosheet which was synthesized very recently for the first time [Nano Lett., 2016, 16, 4903-4908]. The combination of electronic properties of two different two-dimensional materials in an ultrathin van der Waals (vdW) vertical heterostructure has been proved to be an effective approach to the design of novel electronic and optoelectronic devices. Therefore, we used density functional theory to investigate the structural and electronic properties of two BlueP-based heterostructures - BlueP/graphene (BlueP/G) and BlueP/graphene-like gallium nitride (BlueP/g-GaN)...
June 23, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28644188/surgical-techniques-for-total-knee-arthroplasty-measured-resection-gap-balancing-and-hybrid
#7
Neil P Sheth, Adeel Husain, Charles Lenwood Nelson
Total knee arthroplasty (TKA) is effective in managing end-stage degenerative joint disease. Achieving favorable clinical outcomes is predicated on proper implant alignment, sizing, and rotation as well as adequate soft-tissue balancing. Modern TKA implants are designed to address the fundamental needs of attaining stability in both flexion and extension and of optimizing patellar tracking. Measured resection and gap balancing are the two different techniques used to implant the TKA components used today. Both techniques have been validated as durable and successful, and each has unique advantages and disadvantages...
July 2017: Journal of the American Academy of Orthopaedic Surgeons
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#8
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643930/moving-towards-precision-orthodontics-an-evolving-paradigm-shift-in-the-planning-and-delivery-of-customized-orthodontic-therapy
#9
REVIEW
A H Jheon, S Oberoi, R C Solem, S Kapila
Advances in precision medicine portend similar progress in orthodontics and will be increasingly harnessed to achieve customized treatment approaches and enhance treatment efficiencies. Our goal is to provide a background on emerging advances in computer technologies and biomedicine and highlight their current and likely future applications to precision orthodontics. A review of orthodontically relevant technologies and advances in pertinent biological research was undertaken. Innovations in computer hardware and software, and 3D imaging technologies offer the ability for customized treatment and biomechanical planning that will be more fully realized within the next few decades...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643879/inter-subject-alignment-of-meg-datasets-in-a-common-representational-space
#10
Qiong Zhang, Jelmer P Borst, Robert E Kass, John R Anderson
Pooling neural imaging data across subjects requires aligning recordings from different subjects. In magnetoencephalography (MEG) recordings, sensors across subjects are poorly correlated both because of differences in the exact location of the sensors, and structural and functional differences in the brains. It is possible to achieve alignment by assuming that the same regions of different brains correspond across subjects. However, this relies on both the assumption that brain anatomy and function are well correlated, and the strong assumptions that go into solving the under-determined inverse problem given the high-dimensional source space...
June 23, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28643774/insufficient-antibody-validation-challenges-oestrogen-receptor-beta-research
#11
Sandra Andersson, Mårten Sundberg, Nusa Pristovsek, Ahmed Ibrahim, Philip Jonsson, Borbala Katona, Carl-Magnus Clausson, Agata Zieba, Margareta Ramström, Ola Söderberg, Cecilia Williams, Anna Asplund
The discovery of oestrogen receptor β (ERβ/ESR2) was a landmark discovery. Its reported expression and homology with breast cancer pharmacological target ERα (ESR1) raised hopes for improved endocrine therapies. After 20 years of intense research, this has not materialized. We here perform a rigorous validation of 13 anti-ERβ antibodies, using well-characterized controls and a panel of validation methods. We conclude that only one antibody, the rarely used monoclonal PPZ0506, specifically targets ERβ in immunohistochemistry...
June 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643377/randomized-feasibility-trial-to-improve-hydroxyurea-adherence-in-youth-ages-10-18-years-through-community-health-workers-the-habit-study
#12
Nancy S Green, Deepa Manwani, Sergio Matos, April Hicks, Luisa Soto, Yina Castillo, Karen Ireland, Yvonne Stennett, Sally Findley, Haomiao Jia, Arlene Smaldone
INTRODUCTION: The main therapeutic intervention for sickle cell disease (SCD) is hydroxyurea (HU). The effect of HU is largely through dose-dependent induction of fetal hemoglobin (HbF). Poor HU adherence is common among adolescents. METHODS: Our 6-month, two-site pilot intervention trial, "HABIT," was led by culturally aligned community health workers (CHWs). CHWs performed support primarily through home visits, augmented by tailored text message reminders. Dyads of youth with SCD ages 10-18 years and a parent were enrolled...
June 23, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28642775/ectopic-expression-of-the-grape-hyacinth-muscari-armeniacum-r2r3-myb-transcription-factor-gene-maan2-induces-anthocyanin-accumulation-in-tobacco
#13
Kaili Chen, Hongli Liu, Qian Lou, Yali Liu
Anthocyanins are responsible for the different colors of ornamental plants. Grape hyacinth (Muscari armeniacum), a monocot plant with bulbous flowers, is popular for its fascinating blue color. In the present study, we functionally characterized an R2R3-MYB transcription factor gene MaAN2 from M. armeniacum. Our results indicated that MaAN2 participates in controlling anthocyanin biosynthesis. Sequence alignment and phylogenetic analysis suggested that MaAN2 belonged to the R2R3-MYB family AN2 subgroup. The anthocyanin accumulation of grape hyacinth flowers was positively correlated with the expression of MaAN2...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642015/convergent-and-unidirectional-evolution-of-extremely-long-aedeagi-in-the-largest-feather-mite-genus-proctophyllodes-acari-proctophyllodidae-evidence-from-comparative-molecular-and-morphological-phylogenetics
#14
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters...
June 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28641973/changes-in-hip-knee-and-ankle-coronal-alignments-after-total-hip-arthroplasty-with-transverse-femoral-shortening-osteotomy-for-unilateral-crowe-type-iv-developmental-dysplasia-of-the-hip
#15
Abdulhamit Misir, Turan B Kizkapan, Kadir I Yildiz, Mehmet A Kaygusuz, Yakup Alpay, Atakan Ezici
BACKGROUND: To investigate changes in lower extremity coronal alignment in patients with unilateral Crowe type IV developmental dysplasia of the hip who underwent total hip arthroplasty with transverse femoral shortening osteotomy. METHODS: We reviewed the preoperative and 1-year postoperative full-length lower extremity radiographs of 25 patients. Femoral offset (FO), mechanical hip-knee-ankle angle, anatomical axis, mechanical axis deviation (MAD), mechanical lateral proximal femoral angle, anatomical medial proximal femoral angle, mechanical lateral distal femoral angle, anatomical lateral distal femoral angle, knee joint line congruency angle, mechanical medial proximal tibial angle, mechanical lateral distal tibial angle, ankle joint line orientation angle, tibial plafond talus angle, extremity length, and pelvic obliquity were measured on both the operative and nonoperative sides...
June 1, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28641705/citizen-participation-in-health-services-co-production-a-roadmap-for-navigating-participation-types-and-outcomes
#16
Jane Farmer, Judy Taylor, Ellen Stewart, Amanda Kenny
Primary healthcare managers are required to include citizens in service co-design and co-production. Health policy guidance appears deceptively simple and largely outlines how people could participate in a range of health services activities. Policy tends to neglect outcomes assessment, and a multidisciplinary academic literature corpus is large and complex to navigate for practical, time-poor managers. In this paper, we set out to provide a summary 'map' of key concepts in participation to assist managers in aligning participants, activities, expected outcomes and outcome indicators, and to consider contextual factors that could affect participation processes and outcomes...
June 23, 2017: Australian Journal of Primary Health
https://www.readbyqxmd.com/read/28641686/a-case-study-of-human-roll-tilt-perception-in-hypogravity
#17
Torin K Clark, Laurence R Young
BACKGROUND: Increased gravito-inertial acceleration, or hypergravity, such as produced in a centrifuge or in an aircraft coordinated turn, causes humans to systematically overestimate their roll tilt in the dark. This is known as the "G-excess" illusion. We have previously modified a mathematical observer model of dynamic orientation perception to replicate these illusory tilt perceptions. This modified model also made a novel, previously untested, prediction that humans would underestimate acute roll tilt in reduced gravitational environments (hypogravity)...
July 1, 2017: Aerospace Medicine and Human Performance
https://www.readbyqxmd.com/read/28641603/molecular-detection-of-sarcocystis-lutrae-in-the-european-badger-meles-meles-in-scotland
#18
T Lepore, P M Bartley, F Chianini, A I Macrae, E A Innes, F Katzer
Neck samples from 54 badgers and 32 tongue samples of the same badgers (Meles meles), collected in the Lothians and Borders regions of Scotland, were tested using polymerase chain reactions (PCRs) directed against the 18S ribosomal DNA and the internal transcribed spacer (ITS1) region of protozoan parasites of the family Sarcocystidae. Positive results were obtained from 36/54 (67%) neck and 24/32 (75%) tongue samples using an 18S rDNA PCR. A 468 base pair consensus sequence that was generated from the 18S rDNA PCR amplicons (KX229728) showed 100% identity to Sarcocystis lutrae...
June 23, 2017: Parasitology
https://www.readbyqxmd.com/read/28641399/compannotate-a-comparative-approach-to-annotate-base-pairing-interactions-in-rna-3d-structures
#19
Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641265/a-new-method-for-neural-spike-alignment-the-centroid-filter
#20
Benjamin Metcalfe, Chris Clarke, Nick Donaldson, John Taylor
Recordings made directly from the nervous system are a key tool in experimental electrophysiology and the development of bioelectronic medicines. Analysis of these recordings involves the identification of signals from individual neurons, a process known as spike sorting. A critical and limiting feature of spike sorting is the need to align individual spikes in time. However, electrophysiological recordings are made in extremely noisy environments that seriously limit the performance of the spike-alignment process...
June 16, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
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