Miracle-dz/UniFAR-FTUs huggingface dataset:
Nicotinic acetylcholine receptor subunits in rhesus monkey retina.

PURPOSE The purpose of this study was to detect and establish the cellular localizations of nicotinic acetylcholine receptor (nAChR) subunits in Rhesus monkey retina. METHODS Retinas were dissected from the eyes of monkeys killed after unrelated experiments. RNA was extracted and analyzed by RT-PCR, using primers designed against human sequences of alpha3-alpha7, alpha9, and beta2-beta4 nAChR subunits. The RT-PCR products were separated by gel electrophoresis and sequenced. Frozen sections of postmortem fixed monkey eyes were immunolabeled with well-characterized and specific monoclonal antibodies against the alpha3, alpha4, alpha6, alpha7, beta2, or beta4 nAChR subunits and visualized with fluorescence labeling. RESULTS Products of the predicted size for the alpha3-alpha7, alpha9, and beta2-beta4 nAChR subunits were detected by RT-PCR in Rhesus monkey retina. Homology between transcripts from monkey retina and human nucleotide sequences ranged from 93 to 99%. Immunohistochemical studies demonstrated that neurons in various cell layers of monkey retina expressed alpha3, alpha4, alpha7, or beta2 nAChR subunits and cells with the morphology of microglia were immunoreactive for the alpha6 or beta4 nAChR subunits. CONCLUSIONS nAChR subunits are expressed in the monkey retina and localize to diverse retinal neurons as well as putative microglia. Besides mediating visual processing, retinal nAChRs may influence refractive development and ocular pathologies such as neovascularization.
Changes in Neurons and Synapses in Hippocampus of Streptozotocin‐Induced Type 1 Diabetes Rats: A Stereological Investigation

Previous studies have indicated that diabetes could cause hippocampus atrophy, neuron loss, and synaptic plasticity impairment. However, biological conclusions based on density were difficult to interpret because the changes in density could be due to an alteration of total quantity and/or an alteration in the reference volume. In the present study, we used unbiased stereological methods to investigate the effects of type 1 diabetes on the total volume of CA1 and dentate gyrus (DG), the total number of neurons and the total number of Spinophilin/NeurabinII‐positive boutons in CA1 and DG of streptozotocin‐treated rat model. Fifty Sprague–Dawley rats were randomly divided into sodium citrate buffer‐treated group (control group) and streptozotocin (STZ)‐treated group (diabetes group), in which type 1 diabetes was induced by streptozotocin injection. Learning and memory were measured using the Morris water maze test. Our results indicated that diabetes induced deficit in learning/memory, decrease in total CA1 volume (by 51.5%) and degeneration in synaptic structures in CA1sr (by 30.2%). While there were no significant changes in total DG volume, total neuron number in CA1 and DG, total Spinophilin/NeurabinII‐positive bouton number in DG. The present study provided the first evidence of changes in the total volume, the total neuron number and the total Spinophilin/NeurabinII‐positive bouton number in CA1 and DG of STZ‐induced diabetic rats. Anat Rec, 299:1174–1183, 2016. © 2016 Wiley Periodicals, Inc.
P-MaNGA Galaxies: emission-lines properties - gas ionization and chemical abundances from prototype observations

MaNGA (Mapping Nearby Galaxies at Apache Point Observatory) is a 6-yr Sloan Digital Sky Survey (SDSS-IV) survey that will obtain spatially resolved spectroscopy from 3600 to 10 300 A for a representative sample of over 10 000 nearby galaxies. In this paper, we present the analysis of nebular emission-line properties using observations of 14 galaxies obtained with P-MaNGA, a prototype of the MaNGA instrument. By using spatially resolved diagnostic diagrams, we find extended star formation in galaxies that are centrally dominated by Seyfert/LINER-like emission, which illustrates that galaxy characterizations based on single fibre spectra are necessarily incomplete. We observe extended low ionization nuclear emission-line regions (LINER)-like emission (up to 1Re) in the central regions of three galaxies. We make use of the Hα equivalent width [EW(Hα)] to argue that the observed emission is consistent with ionization from hot evolved stars. We derive stellar population indices and demonstrate a clear correlation between Dn(4000) and EW(HδA) and the position in the ionization diagnostic diagram: resolved galactic regions which are ionized by a Seyfert/LINER-like radiation field are also devoid of recent star formation and host older and/or more metal-rich stellar populations. We also detect extraplanar LINER-like emission in two highly inclined galaxies, and identify it with diffuse ionized gas. We investigate spatially resolved metallicities and find a positive correlation between metallicity and star formation rate surface density. We further study the relation between N/O versus O/H on resolved scales. We find that, at given N/O, regions within individual galaxies are spread towards lower metallicities, deviating from the sequence defined by galactic central regions as traced by Sloan 3-arcsec fibre spectra. We suggest that the observed dispersion can be a tracer for gas flows in galaxies: infalls of pristine gas and/or the effect of a galactic fountain.
Passive Plasmonic Demultiplexers Using Multimode Interference

Two passive plasmonic demultiplexers with multimode interferometer (MMI) based rectangular and bow-tie designs are demonstrated for 1.31- and 1.55-μm-band wavelength division multiplexing system operation in plasmonic circuits. These demultiplexers are designed using the finite-difference time-domain (FDTD) method and fabricated using complementary metal–oxide–semiconductor compatible processes. SiO2 films deposited on metal films are etched to form mesa structures by focused ion beam milling, and single-mode waveguides, MMIs, and bow-tie structures are then formed on the metal films. In the plasmonic circuits, 1.31- or 1.55-μm-wavelength surface plasmon polariton (SPP) signals can be distributed to each of the different demultiplexer outputs without any change in signal propagation speed. The SPP intensity distributions that are measured using a scanning near-field optical microscope agree well with the distributions that were calculated using the FDTD method. The insertion loss and crosstalk are then calculated for each demultiplexer. In the rectangular-type demultiplexer, the calculated values were less than 9.5 dB and –2.4 dB, and in the bow-tie-type demultiplexer, the corresponding values were 8.9 dB and less than –2.3 dB, respectively. These results demonstrate the applicability of the developed plasmonic demultiplexers to plasmonic circuits when monolithically integrated on a silicon substrate.
The benthic foraminiferal community in a naturally CO 2 -rich coastal habitat of the southwestern Baltic Sea

Abstract. It is expected that the calcification of foraminifera will be negatively affected by the ongoing acidification of the oceans. Compared to the open oceans, these organisms are subjected to much more adverse carbonate system conditions in coastal and estuarine environments such as the southwestern Baltic Sea, where benthic foraminifera are abundant. This study documents the seasonal changes of carbonate chemistry and the ensuing response of the foraminiferal community with bi-monthly resolution in Flensburg Fjord. In comparison to the surface pCO2, which is close to equilibrium with the atmosphere, we observed large seasonal fluctuations of pCO2 in the bottom and sediment pore waters. The sediment pore water pCO2 was constantly high during the entire year ranging from 1244 to 3324 μatm. Nevertheless, in contrast to the bottom water, sediment pore water was slightly supersaturated with respect to calcite as a consequence of higher alkalinity (AT) for most of the year. Foraminiferal assemblages were dominated by two calcareous species, Ammonia aomoriensis and Elphidium incertum, and the agglutinated Ammotium cassis. The one-year cycle was characterised by seasonal community shifts. Our results revealed that there is no dynamic response of foraminiferal population density and diversity to elevated sediment pore water pCO2. Surprisingly, the fluctuations of sediment pore water undersaturation (Ωcalc) co-vary with the population densities of living Ammonia aomoriensis. Further, we observed that most of the tests of living calcifying foraminifera were intact. Only Ammonia aomorienis showed dissolution and recalcification structures on the tests, especially at undersaturated conditions. Therefore, the benthic community is subjected to high pCO2 and tolerates elevated levels as long as sediment pore water remains supersaturated. Model calculations inferred that increasing atmospheric CO2 concentrations will finally lead to a perennial undersaturation in sediment pore waters. Whereas benthic foraminifera indeed may cope with a high sediment pore water pCO2, the steady undersaturation of sediment pore waters would likely cause a significant higher mortality of the dominating Ammonia aomoriensis. This shift may eventually lead to changes in the benthic foraminiferal communities in Flensburg Fjord, as well as in other regions experiencing naturally undersaturated Ωcalc levels.
Specialized Interior-Point Algorithm for Stable Nonlinear System Identification

Estimation of nonlinear dynamic models from data poses many challenges, including model instability and nonconvexity of long-term simulation fidelity. Recently Lagrangian relaxation has been proposed as a method to approximate simulation fidelity and guarantee stability via semidefinite programming (SDP); however, the resulting SDPs have large dimension, limiting their utility in practical problems. In this paper, we develop a path-following interior-point algorithm that takes advantage of special structure in the problem and reduces computational complexity from cubic to linear growth with the length of the dataset. The new algorithm enables empirical comparisons to established methods including nonlinear autoregressive models with exogenous inputs, and we demonstrate superior generalization to new data. We also explore the “regularizing” effect of stability constraints as an alternative to regressor subset selection.
Epidemiology and Impact of Scarring After Burn Injury: A Systematic Review of the Literature

The purpose of this study was to perform a systematic review of the existing literature on the incidence of hypertrophic scarring and the psychosocial impact of burn scars. In a comprehensive literature review, the authors identified 48 articles published since 1965 and written in English which reported the incidence and risk factors for hypertrophic scarring or assessed outcomes related to scarring. Most studies had important methodological limitations limiting the generalizability of the findings. In particular, the absence of standardized valid measures of scarring and other outcome variables was a major barrier to drawing strong conclusions. Among studies on hypertrophic scarring, the prevalence rate varied between 32 and 72%. Identified risk factors included dark skin, female gender, young age, burn site on neck and upper limb, multiple surgical procedures, meshed skin graph, time to healing, and burn severity. With regard to psychosocial outcomes, two studies compared pediatric burn survivors with a nonburn comparison group on a body image measure; neither study found differences between groups. Across studies, burn severity and location had a modest relationship with psychosocial outcome variables. Psychosocial variables such as social comfort and perceived stigmatization were more highly associated with body image than burn characteristics. To advance our knowledge of the epidemiology of scars and the burden of scars, future studies need to implement more rigorous methodologies. In particular, standardized valid measures of scarring and other outcomes should be developed. This process could be facilitated by an international collaboration among burn centers.
Appropriateness of Prostate Cancer Imaging among Veterans in a Delivery System without Incentives for Overutilization.

OBJECTIVE To determine the frequency of appropriate and inappropriate prostate cancer imaging in an integrated health care system. DATA SOURCES/STUDY SETTING Veterans Health Administration Central Cancer Registry linked to VA electronic medical records and Medicare claims (2004-2008). STUDY DESIGN We performed a retrospective cohort study of VA patients diagnosed with prostate cancer (N = 45,084). Imaging (CT, MRI, bone scan, PET) use was assessed among patients with low-risk disease, for whom guidelines recommend against advanced imaging, and among high-risk patients for whom guidelines recommend it. PRINCIPAL FINDINGS We found high rates of inappropriate imaging among men with low-risk prostate cancer (41 percent) and suboptimal rates of appropriate imaging among men with high-risk disease (70 percent). Veterans utilizing Medicare-reimbursed care had higher rates of inappropriate imaging [OR: 1.09 (1.03-1.16)] but not higher rates of appropriate imaging. Veterans treated in middle [OR: 0.51 (0.47-0.56)] and higher [OR: 0.50 (0.46-0.55)] volume medical centers were less likely to undergo inappropriate imaging without compromising appropriate imaging. CONCLUSIONS Our results highlight the overutilization of imaging, even in an integrated health care system without financial incentives encouraging provision of health care services. Paradoxically, imaging remains underutilized among high-risk patients who could potentially benefit from it most.
A kinematics-dynamics based estimator of the center of mass position for anthropomorphic system — A complementary filtering approach

This paper presents an original approach to simply and efficiently estimate the center of mass position of a free-floating base system, like a humanoid robot or a human body. This approach relies on the theory of complementary filtering, which is a popular technique in aerial robotics, but rarely implemented in humanoid robotics. The main idea consists in merging input measurements like the zero-moment point position, the contact forces, etc. which are then filtered according to their reliability in their respective spectral bandwidth. We validate this approach in simulation by (i) comparing the estimated center of mass trajectory with its real value and (ii) showing that the complementary filter offers on average a least reconstruction error than the classic Kalman filter.
PySEAL: A Python wrapper implementation of the SEAL homomorphic encryption library

Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully homomorphic encryption developed in C++ by Microsoft Research. Despite the advantages of C++, Python is a flexible and dominant programming language that enables rapid prototyping of bioinformatics pipelines. Results: In an effort to make homomorphic encryption accessible to a broader range of bioinformatics scientists and applications, we present a Python binding implementation of the popular homomorphic encryption library, SEAL, using pybind11. The software contains a Docker image to facilitate easy installation and execution of the SEAL build process. Availability: All code is publicly available at this https URL Contact: lab41@iqt.org Supplementary information: Supplementary information is available on the Lab41 GitHub.
Vibro-tactile and auditory balance biofeedback changes muscle activity patterns: Possible implications for vestibular implants.

BACKGROUND The two different types of balance prostheses being developed, implants and vibro-tactile/auditory feedback prostheses, rely on different measures to prove efficacy (those based on vestibular ocular reflexes versus balance control, respectively). Here we provide evidence that examining muscle activity might provide a useful alternative for both. METHODS The muscle activity of 6 bilateral vestibular loss (BVL) and 7 age-matched healthy controls (HC) was examined while standing eyes closed on a foam support surface. Pelvis and upper trunk angular movements were recorded in the roll and pitch planes. Surface EMG was recorded from the lower leg, trunk and upper arm muscles. BVL subjects were first assessed without feedback of pelvis sway, then received training with combined vibro-tactile and auditory feedback, before being re-assessed with feedback. RESULTS Feedback reduced the amplitudes of pelvis and shoulder sway to values of HC without feedback. Both the level of background EMG activity and the EMG area amplitudes changed when feedback was provided in a manner consistent with the reduced amplitude modulation of muscle synergies of HC. CONCLUSIONS The results of this study indicate that changed muscle synergy amplitudes underlie improvements in sway achieved by BVL subjects. The concept of this investigation may provide a means to prove efficacy for different types of balance prostheses, including implants.
Enhancement of Electrical Properties of Ferroelectric Polymers by Polyaniline Nanofibers with Controllable Conductivities

Conductive nanofibers are adopted to enhance the electric properties of ferroelectric polymers. Polyaniline (PANI) nanofibers doped by protonic acids have a high dispersion stability in vinylidene fluoride‐trifluoroethylene copolymers [P(VDF‐TrFE)] and lead to percolative nanocomposites with enhanced electric responses. About a 50‐fold rise in the dielectric constant of the ferroelectric polymer matrix has been achieved. Percolation thresholds of the nanocomposites are relevant to doping levels of PANI nanofibers and can be as low as 2.9 wt% for fully doped nanofibers. The interface between the conductive nanofiber and the polymer matrix plays a crucial role in the dielectric enhancement of the nanocomposites in the vicinity of the percolation threshold. Compared with other dopants, perfluorosulfonic acid resin is better at improving the performance of the nanofibers in that it serves as a surface passivation layer for the conductive fillers and suppresses leakage current at low frequency. The nanofibers drastically reduce the electric field strength required to switch spontaneous polarization of P(VDF‐TrFE). The nanocomposites can be utilized for potential applications as high energy density capacitors, thin‐film transistors, and non‐volatile ferroelectric memories.
Dietary fibre alleviates hepatic fat deposition via inhibiting lipogenic gene expression in meat ducks

This study investigated the effect of dietary fibre (DF) supplementation on hepatic fat deposition of Cherry Valley meat ducks. A total of 600 1-d-old ducks were randomly allotted to five dietary fibre diets (1.46 (basal diet), 3.09, 4.15, 6.18 and 7.52% (analysed)) for 14 days. Growth performance decreased with increasing DF concentrations, when the DF level more than 6.18% the average daily gain (ADG) and feed conversion ratio (F/G) markedly decreased in meat ducks. Meat ducks supplemented over 4.15% DF had lower percentage of liver reported to live weight, liver lipid contents, hepatic triglyceride and total cholesterol concentrations as well as decreased serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) concentrations at 14 days. The transcription of fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC) and sterol-regulatory element-binding protein-1 (SREBP-1) in liver was significantly reduced by DF, while no any significant difference was found about the effect of DF on hepatic peroxisome proliferator-activated receptor α (PPARα), adipose triglyceride lipase (ATGL), transcription as well as caecal digesta short-chain fatty acids (SCFA). Data suggested that dietary fibre supplementation decreased hepatic lipid deposition and improved characteristics of liver health via inhibiting hepatic FAS, ACC and SREBP-1 expression in meat ducks.
Type‐1 interferons contribute to the neuroinflammatory response and disease progression of the MPTP mouse model of Parkinson's disease

Type‐1 interferons (IFNs) are pleiotropic cytokines with a critical role in the initiation and regulation of the pro‐inflammatory response. However, the contribution of the type‐1 IFNs to CNS disorders, specifically chronic neuropathologies such as Parkinson's disease is still unknown. Here, we report increased type‐1 IFN signaling in both post mortem human Parkinson's disease samples and in the 1‐methyl‐4‐phenyl‐1, 2, 3, 6‐tetrahydropyridine (MPTP) mouse model. In response to MPTP, mice lacking the type‐1 IFN receptor (IFNAR1−/−) displayed decreased type‐1 IFN signaling, an attenuated pro‐inflammatory response and reduced loss of dopaminergic neurons. The neuroprotective potential of targeting the type‐1 IFN pathway was confirmed by reduced neuroinflammation and DA cell death in mice treated with a blocking monoclonal IFNAR1 (MAR‐1) antibody. The MPTP/MAR‐1 treated mice also displayed increased striatal dopamine levels and improved behavioural outcomes compared to their MPTP/IgG controls. These data, implicate for the first time, a deleterious role for the type‐1 IFNs as key modulators of the early neuroinflammatory response and therefore the neuronal cell death in Parkinson's disease. GLIA 2016;64:1590–1604
Salivary human beta-defensins affected by oral Candida status in Chinese HIV/AIDS patients undergoing ART.

OBJECTIVES To observe relationships between oral Candida status and salivary human beta-defensin 2 and 3 (hBD-2 and hBD-3) levels in HIV/AIDS patients of Guangxi, China during the first year of antiretroviral therapy (ART) dynamically, and to understand the influence of ART on oral Candida status and salivary hBDs expressions. METHODS A prospective self-controlled study was carried to observe the dynamic changes of CD4+ T cell counts, oral Candida carriages and salivary hBD-2,3 expressions in HIV/AIDS patients during the first year of ART. A total of 90 HIV/AIDS patients were enrolled and were examined at the baseline, 3rd, 6th, 12th month of ART. Thirty healthy individuals were enrolled as control. Peripheral blood, oral rinse sample, and unstimulated whole saliva were collected to test CD4+ T cell counts, oral Candida carriages, and hBD-2,3 expressions. RESULTS In the first year of ART, CD4+ T cell counts increased significantly. However, oral Candida carriages and oral candidiasis decreased significantly, and salivary hBD-2 expressions in HIV/AIDS patients decreased gradually, salivary hBD-3 levels were highly variable. Salivary hBD-2 concentrations were positively related to oral Candida carriages. CONCLUSIONS The incidence of oral candidiasis among HIV/AIDS patients gradually decreased due to the immune reconstruction of ART. Salivary defensins might play an important role in Candida-host interaction in HIV/AIDS patients.
Identity-Based Format-Preserving Encryption

We introduce identity-based format-preserving encryption (IB-FPE) as a way to localize and limit the damage to format-preserving encryption (FPE) from key exposure. We give definitions, relations between them, generic attacks and two transforms of FPE schemes to IB-FPE schemes. As a special case, we introduce and cover identity-based tweakable blockciphers. We apply all this to analyze DFF, an FPE scheme proposed to NIST for standardization.