Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Dengue and Zika Outbreaks Reveals Differences by Setting and Virus

The pacific islands of Micronesia have experienced several outbreaks of mosquito-borne diseases over the past decade. In outbreaks on small islands, the susceptible population is usually well defined, and there is no co-circulation of pathogens. Because of this, analysing such outbreaks can be useful for understanding the transmission dynamics of the pathogens involved, and particularly so for yet understudied pathogens such as Zika virus. Here, we compared three outbreaks of dengue and Zika virus in two different island settings in Micronesia, the Yap Main Islands and Fais, using a mathematical model of transmission dynamics, making full use of commonalities in disease and setting between the outbreaks. We found that the estimated reproduction numbers for Zika and dengue were similar when considered in the same setting, but that, conversely, reproduction number for the same disease can vary considerably by setting. On the Yap Main Islands, we estimated a reproduction number of 8.0–16 (95% Credible Interval (CI)) for the dengue outbreak and 4.8–14 (95% CI) for the Zika outbreak, whereas for the dengue outbreak on Fais our estimate was 28–102 (95% CI). We further found that the proportion of cases of Zika reported was smaller (95% CI 1.4%–1.9%) than that of dengue (95% CI 47%–61%). We confirmed these results in extensive sensitivity analysis. They suggest that models for dengue transmission can be useful for estimating the predicted dynamics of Zika transmission, but care must be taken when extrapolating findings from one setting to another. Author Summary Dengue and Zika are related viruses and are both transmitted by mosquitoes. Dengue is well described and affects people around the world. Zika, on the other hand has only recently caused outbreak in human populations, and it has been suggested that its behaviour might similar dengue. To investigate this, we compared three outbreaks of dengue and Zika in island populations of the pacific: two dengue outbreaks and one Zika outbreak. Island outbreaks are useful laboratories for understanding the spread of infections because they are usually short, well-identified episodes, whereas elsewhere it can be difficult to identify the properties of outbreaks when different viruses spread at the same time. In our investigation of the outbreaks in Micronesia we found that dengue and Zika virus did, indeed, behave similar in outbreaks they caused on the Yap Main Islands. A dengue outbreak on the smaller island of Fais, on the other hand, was different from the dengue outbreak on Yap in that transmission seems to have been more efficient. We conclude that dengue outbreaks are indeed a good model for Zika outbreaks when considered in the same setting, but that one must be careful when comparing outbreaks in different settings.
Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications

Lipid transfer proteins (LTPs) are a family of proteins that bind and transfer lipids. Utilizing the maize LTP, we have successfully engineered fluorescent reagentless biosensors for the natural ligand of LTPs; this was achieved by using computational protein design to remove a disulfide bridge and attaching a thio‐reactive fluorophore. Conformational change induced by ligand titration is thought to affect the fluorescence of the fluorophore, allowing detection of ligand binding. Fluorescence measurements show that our LTP variants have affinity to palmitate that is consistent with wild‐type LTP. These molecules have the potential to be utilized as scaffolds to design hydrophobic ligand biosensors or to serve as drug carriers.
The roles of receptor and ligand endocytosis in regulating Notch signaling

Cell-cell signaling is a central process in the formation of multicellular organisms. Notch (N) is the receptor of a conserved signaling pathway that regulates numerous developmental decisions, and the misregulation of N has been linked to various physiological and developmental disorders. The endocytosis of N and its ligands is a key mechanism by which N-mediated cell-cell signaling is developmentally regulated. We review here the recent findings that have highlighted the importance and complexity of this regulation.
Estimation of hormone receptor status in fine‐needle aspirates and paraffin‐embedded sections from breast cancer using the novel rabbit monoclonal antibodies SP1 and SP2

We describe a method of immunocytochemical assessment of estrogen receptor (ER) status on alcohol‐fixed smears obtained by fine‐needle aspiration (FNA) from breast cancer patients, using a commercially available rabbit monoclonal antibody anti‐ER (SP1) without any antigen retrieval. A series of 40 aspirates were analyzed and the results of ER status were compared with the respective formalin‐fixed tissue using the same procedure and with assessment by the classical method using the mouse monoclonal antibody 6F11 (anti‐ER) with antigen retrieval on paraffin sections. Twenty‐four out of the 40 cases examined were positive at least by two methods and 16 were negative for all three determinations. The results obtained in the ER immunocytochemical assay on aspirates and paraffin sections using the antibody SP1 and those obtained on paraffin sections using the antibody 6F11 were quite similar. In one case the material was insufficient to interpret the reaction in the cytological specimen and only one case, with focal positivity reaction on paraffin sections, was negative in the cytological specimen. The intensity of nuclei staining in cytological smears of breast cancer cells was stronger than that observed by traditional methods. We also assessed progesterone receptor (PR) status on 40 paraffin‐sections from breast cancer patients, using a commercially available rabbit monoclonal antibody anti‐PR (SP2), with the same characteristics described for anti‐ER (SP1). The results were compared with assessment by the classic method with mouse monoclonal antibody 1A6 (PR) on paraffin sections and total agreement was observed. Of the 40 cases examined, 18 were positive and 22 were negative for the two determinations. We conclude that the application of the ER method on alcohol‐fixed smears / paraffin sections with the rabbit monoclonal antibody SP1, and the PR method on paraffin sections with the rabbit monoclonal antibody SP2, provide several advantages, such as high sensitivity and specificity of the reaction, stronger immunostaining, shorter procedures times, and avoidance of antigenic retrieval methods. Diagn. Cytopathol. 2003;29:207–211. © 2003 Wiley‐Liss, Inc.
Early palliative care for patients with metastatic non-small-cell lung cancer.

BACKGROUND Patients with metastatic non-small-cell lung cancer have a substantial symptom burden and may receive aggressive care at the end of life. We examined the effect of introducing palliative care early after diagnosis on patient-reported outcomes and end-of-life care among ambulatory patients with newly diagnosed disease. METHODS We randomly assigned patients with newly diagnosed metastatic non-small-cell lung cancer to receive either early palliative care integrated with standard oncologic care or standard oncologic care alone. Quality of life and mood were assessed at baseline and at 12 weeks with the use of the Functional Assessment of Cancer Therapy-Lung (FACT-L) scale and the Hospital Anxiety and Depression Scale, respectively. The primary outcome was the change in the quality of life at 12 weeks. Data on end-of-life care were collected from electronic medical records. RESULTS Of the 151 patients who underwent randomization, 27 died by 12 weeks and 107 (86% of the remaining patients) completed assessments. Patients assigned to early palliative care had a better quality of life than did patients assigned to standard care (mean score on the FACT-L scale [in which scores range from 0 to 136, with higher scores indicating better quality of life], 98.0 vs. 91.5; P=0.03). In addition, fewer patients in the palliative care group than in the standard care group had depressive symptoms (16% vs. 38%, P=0.01). Despite the fact that fewer patients in the early palliative care group than in the standard care group received aggressive end-of-life care (33% vs. 54%, P=0.05), median survival was longer among patients receiving early palliative care (11.6 months vs. 8.9 months, P=0.02). CONCLUSIONS Among patients with metastatic non-small-cell lung cancer, early palliative care led to significant improvements in both quality of life and mood. As compared with patients receiving standard care, patients receiving early palliative care had less aggressive care at the end of life but longer survival. (Funded by an American Society of Clinical Oncology Career Development Award and philanthropic gifts; ClinicalTrials.gov number, NCT01038271.)
Norges Teknisk-naturvitenskapelige Universitet Approximating Hidden Gaussian Markov Random Fields Approximating Hidden Gaussian Markov Random Fields

This paper discusses how to construct approximations to a unimodal hidden Gaussian Markov random field on a graph of dimension Ò when the likelihood consists of mutually independent data. We demonstrate that a class of non-Gaussian approximations can be constructed for a wide range of likelihood models. They have the appealing properties that exact samples can be drawn from them, the normalisation constant is computable, and the computational complexity is only Ç´Ò ¾ µ in the spatial case. The non-Gaussian approximations are refined versions of a Gaussian approximation. The latter serves well if the likelihood is near-Gaussian, but it is not sufficiently accurate when the likelihood is not near-Gaussian or if Ò is large. The accuracy of our approximations can be tuned by intuitive parameters to near any precision. We apply our approximations in spatial disease mapping and model-based geostatistics models with different likelihoods. We also present procedures for block-updating and construction of Metropolised independence samplers for such models. These sampling schemes are major improvements compared to the single-site schemes commonly used.
The Performance of Index Based Livestock Insurance: Ex Ante Assessment in the Presence of a Poverty Trap

This paper evaluates the effectiveness of a new index-based livestock insurance (IBLI) product designed to compensate for area average predicted livestock mortality loss in northern Kenya, where previous work has established the presence of poverty traps. We simulate household-specific wealth dynamics based on a model parameterized using rich panel and experimental data from the region. The simulations allow us to investigate patterns of willingness to pay for asset index insurance that is imperfectly correlated with individuals' loss experience. The bifurcated livestock dynamics associated with the poverty trap gives rise to insurance valuation that is highly nonlinear in individual herd size. Willingness to pay among vulnerable groups who most need insurance are, on average, lower than commercially viable rates but subsidization of IBLI premiums appears to offer more cost-effective poverty reduction than direct transfers to the poor.
Transport theories for heavy-ion collisions in the 1 A GeV regime

We compare multiplicities as well as rapidity and transverse momentum distributions of protons, pions and kaons calculated within presently available transport approaches for heavy-ion collisions around 1 A GeV. For this purpose, three reactions have been selected: Au+Au at 1 and 1.48 A GeV and Ni+Ni at 1.93 A GeV.
Mental health of the mothers of malnourished children.

BACKGROUND The objective of this study is to measure the association between protein-energy malnutrition (PEM) in children and their mothers' mental health, in a low income area in the city of Embú, São Paulo, Brazil. METHODS A case-control study was performed. Cases were 60 moderately and severely malnourished children (Gomez criteria) selected from two primary health care units. Controls consisted of 45 eutrophic children attending the same units. The main outcome measure was for the mothers to present a mental health score > 6 according with the 'Adult Psychiatric Morbidity Questionnaire' (QMPA), a psychiatric screening instrument. RESULTS Of mothers of children with PEM, 63% and 38% of mothers in the control group were QMPA positive: odds ratio (OR) = 2.8 (95% confidence interval [CI]: 1.2-6.9). Of PEM children, 27% had low birthweight (LBW = < 2500 g) and 6% of the control group had LBW. Interactions were found between: mothers' mental health and number of children (with > or = 4 children: OR = 20.0 [95% CI: 2.1-274.2], with < or = 3 children: OR = 1.6 [95% CI: 0.6-4.5), as well as mothers' mental health and maternal age (in women > 30: OR = 12.5 [95% CI: 2.0-93.4], in women < or = 30: OR = 1.5 [95% CI: 0.5-4.4]. CONCLUSIONS Mothers of children with PEM showed a higher rate of mental disturbances than mothers of eutrophic children. Unlike LBW, maternal age and number of children interact with mothers' mental health, increasing the association. Management of poor mental health may lead to mothers being better caretakers of their children and this may have a positive impact on PEM.
North Pacific Paleotemperature and Paleoproductivity Reconstructions Based on Diatom Species

Regionally developed diatom‐based transfer functions reconstruct both summer sea surface temperature and primary productivity (PP) in the North Pacific based on a calibration data set including the eastern subtropical gyre (California and Oregon), the Gulf of Alaska, the western Pacific, and Bering Sea. Factors of the floral assemblage and environment data sets, and canonical correspondence, support estimation of two essentially orthogonal variables. Validation of the summer sea surface temperature transfer function resulted in r2jack of 0.9 and a root‐mean‐square error of prediction of 1.0°C over a range of 7–17°C. The summer PP transfer function yielded r2jack of 0.7 and a root‐mean‐square error of prediction of 219 g C·m2·year over a range of 200–2,000 g C·m2·year. Application in downcore locations within the modern nearshore upwelling regime and within the California Current offshore Oregon reveals that during Holocene time higher PP (>800 g C·m2·year) was associated with cooler temperatures (<16°C) forced by upwelling. In contrast, during the Last Glacial Maximum, when subpolar conditions are present off Oregon, higher PP (>1,000 g C·m2·year) was associated with warmer SSTs (>10°C; significant in the nearshore site). This finding supports previous hypotheses that in cold regimes warming may augment biological production, perhaps by relieving metabolic constraints. This is of particular interest because of projected amplification of future warming in high latitudes and the potential for greening of the subpolar and polar oceans.
Quantification of Mesenchymal Stem Cell (MSC) Delivery to a Target Site Using In Vivo Confocal Microscopy

The ability to deliver cells to appropriate target tissues is a prerequisite for successful cell-based therapy. To optimize cell therapy it is therefore necessary to develop a robust method of in vivo cell delivery quantification. Here we examine Mesenchymal Stem Cells (MSCs) labeled with a series of 4 membrane dyes from which we select the optimal dye combination for pair-wise comparisons of delivery to inflamed tissue in the mouse ear using confocal fluorescence imaging. The use of an optimized dye pair for simultaneous tracking of two cell populations in the same animal enables quantification of a test population that is referenced to an internal control population, thereby eliminating intra-subject variations and variations in injected cell numbers. Consistent results were obtained even when the administered cell number varied by more than an order of magnitude, demonstrating an ability to neutralize one of the largest sources of in vivo experimental error and to greatly reduce the number of cells required to evaluate cell delivery. With this method, we are able to show a small but significant increase in the delivery of cytokine pre-treated MSCs (TNF-α & IFN-γ) compared to control MSCs. Our results suggest future directions for screening cell strategies using our in vivo cell delivery assay, which may be useful to develop methods to maximize cell therapeutic potential.
Differentiating Radiation-Induced Necrosis from Recurrent Brain Tumor Using MR Perfusion and Spectroscopy: A Meta-Analysis

Purpose This meta-analysis examined roles of several metabolites in differentiating recurrent tumor from necrosis in patients with brain tumors using MR perfusion and spectroscopy. Methods Medline, Cochrane, EMBASE, and Google Scholar were searched for studies using perfusion MRI and/or MR spectroscopy published up to March 4, 2015 which differentiated between recurrent tumor vs. necrosis in patients with primary brain tumors or brain metastasis. Only two-armed, prospective or retrospective studies were included. A meta-analysis was performed on the difference in relative cerebral blood volume (rCBV), ratios of choline/creatine (Cho/Cr) and/or choline/N-acetyl aspartate (Cho/NAA) between participants undergoing MRI evaluation. A χ2-based test of homogeneity was performed using Cochran’s Q statistic and I2. Results Of 397 patients in 13 studies who were analyzed, the majority had tumor recurrence. As there was evidence of heterogeneity among 10 of the studies which used rCBV for evaluation (Q statistic = 31.634, I2 = 97.11%, P < 0.0001) a random-effects analysis was applied. The pooled difference in means (2.18, 95%CI = 0.85 to 3.50) indicated that the average rCBV in a contrast-enhancing lesion was significantly higher in tumor recurrence compared with radiation injury (P = 0.001). Based on a fixed-effect model of analysis encompassing the six studies which used Cho/Cr ratios for evaluation (Q statistic = 8.388, I2 = 40.39%, P = 0.137), the pooled difference in means (0.77, 95%CI = 0.57 to 0.98) of the average Cho/Cr ratio was significantly higher in tumor recurrence than in tumor necrosis (P = 0.001). There was significant difference in ratios of Cho to NAA between recurrent tumor and necrosis (1.02, 95%CI = 0.03 to 2.00, P = 0.044). Conclusions MR spectroscopy and MR perfusion using Cho/NAA and Cho/Cr ratios and rCBV may increase the accuracy of differentiating necrosis from recurrent tumor in patients with primary brain tumors or metastases.
Aggregation With Fragment Retransmission for Very High-Speed WLANs

In upcoming very high-speed wireless LANs (WLANs), the physical (PHY) layer rate may reach 600 Mbps. To achieve high efficiency at the medium access control (MAC) layer, we identify fundamental properties that must be satisfied by any CSMA-/CA-based MAC layers and develop a novel scheme called aggregation with fragment retransmission (AFR) that exhibits these properties. In the AFR scheme, multiple packets are aggregated into and transmitted in a single large frame. If errors happen during the transmission, only the corrupted fragments of the large frame are retransmitted. An analytic model is developed to evaluate the throughput and delay performance of AFR over noisy channels and to compare AFR with similar schemes in the literature. Optimal frame and fragment sizes are calculated using this model. Transmission delays are minimized by using a zero-waiting mechanism where frames are transmitted immediately once the MAC wins a transmission opportunity. We prove that zero-waiting can achieve maximum throughput. As a complement to the theoretical analysis, we investigate the impact of AFR on the performance of realistic application traffic with diverse requirements by simulations. We have implemented the AFR scheme in the NS-2 simulator and present detailed results for TCP, VoIP, and HDTV traffic. The AFR scheme described was developed as part of the IEEE 802.11n working group work. The analysis presented here is general enough to be extended to proposed schemes in the upcoming 802.11n standard. Trends indicated in this paper should extend to any well-designed aggregation schemes.
The effects of the glycine reuptake inhibitor R213129 on the central nervous system and on scopolamine-induced impairments in psychomotor and cognitive function in healthy subjects

In this study the effects of R213129, a selective glycine transporter 1 inhibitor, on central nervous system function were investigated in healthy males in the absence and presence of scopolamine. This was a double-blind, placebo-controlled, 4-period crossover ascending dose study evaluating the following endpoints: body sway, saccadic and smooth pursuit eye movements, pupillometry, electroencephalography, visual analogue scales for alertness, mood, calmness and psychedelic effects, adaptive tracking, finger tapping, Visual and Verbal Learning Task, Stroop test, hormone levels and pharmacokinetics. R213129 dose levels were selected based on exposure levels that blocked the GlyT1 sites >50% in preclinical experiments. Forty-three of the 45 included subjects completed the study. Scopolamine significantly affected almost every central nervous system parameter measured in this study. R213129 alone compared with placebo did not elicit pharmacodynamic changes. R213129 had some small effects on scopolamine-induced central nervous system impairments. Scopolamine-induced finger tapping impairment was further enhanced by 3 mg R213129 with 2.0 taps/10 seconds (95% CI -4.0, -0.1), electroencephalography alpha power was increased by 10 mg R213129 with respectively 12.9% (0.7, 26.6%), scopolamine-induced impairment of the Stroop test was partly reversed by 10 mg R213129 with 59 milliseconds (-110, -7). Scopolamine produced robust and consistent effects in psychomotor and cognitive function in healthy volunteers. The most logical reason for the lack of R213129 effects seems to be that the central nervous system concentrations were too low. The effects of higher doses in healthy volunteers and the clinical efficacy in patients remain to be established.
Resting-State Brain Organization Revealed by Functional Covariance Networks

Background Brain network studies using techniques of intrinsic connectivity network based on fMRI time series (TS-ICN) and structural covariance network (SCN) have mapped out functional and structural organization of human brain at respective time scales. However, there lacks a meso-time-scale network to bridge the ICN and SCN and get insights of brain functional organization. Methodology and Principal Findings We proposed a functional covariance network (FCN) method by measuring the covariance of amplitude of low-frequency fluctuations (ALFF) in BOLD signals across subjects, and compared the patterns of ALFF-FCNs with the TS-ICNs and SCNs by mapping the brain networks of default network, task-positive network and sensory networks. We demonstrated large overlap among FCNs, ICNs and SCNs and modular nature in FCNs and ICNs by using conjunctional analysis. Most interestingly, FCN analysis showed a network dichotomy consisting of anti-correlated high-level cognitive system and low-level perceptive system, which is a novel finding different from the ICN dichotomy consisting of the default-mode network and the task-positive network. Conclusion The current study proposed an ALFF-FCN approach to measure the interregional correlation of brain activity responding to short periods of state, and revealed novel organization patterns of resting-state brain activity from an intermediate time scale.