Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Estimation of Firing Rates from Calcium Imaging Data

Two-photon imaging of calcium indicators allows simultaneous recording of responses of hundreds of neurons over hours and even days, but provides a relatively indirect measure of their spiking activity. Existing deconvolution algorithms attempt to recover spikes from observed imaging data, which are then commonly subjected to the same analyses that are applied to electrophysiologically recorded spikes (e.g., estimation of average firing rates, or tuning curves). Here we show, however, that in the presence of noise this approach is often heavily biased. We propose an alternative analysis that aims to estimate the underlying rate directly, by integrating over the unobserved spikes instead of committing to a single estimate of the spike train. This approach can be used to estimate average firing rates or tuning curves directly from the imaging data, and is sufficiently flexible to incorporate prior knowledge about tuning structure. We show that directly estimated rates are more accurate than those obtained from averaging of spikes estimated through deconvolution, both on simulated data and on imaging data acquired in mouse visual cortex.
Detecting Planets around Compact Binaries with Gravitational Wave Detectors in Space

I propose a method to detect planets around compact binaries that are strong sources of gravitational radiation. This approach is to measure gravitational wave phase modulations induced by the planets, and its prospect is studied with a Fisher matrix analysis. I find that, using LISA, planets can be searched for around ~3000 Galactic double white dwarfs with detection limit ≳ 4 MJ (MJ ∼ 2 × 1030 g: the Jupiter mass). With its follow-on missions, planets with mass ≳ 1 MJ might be detected around double neutron stars even at cosmological distances z ∼ 1. In this manner, gravitational wave observation has the potential to make interesting contributions to extrasolar planetary science.
Implementation study of Hybrid caching scheme in Wireless P 2 P networks with Asymmetric Cooperative caching

As the day to day applications in mobile computing are increasing, different wireless peer-peer networks came into existence. There are several protocols and schemes are implemented to increase the network performance. The most implemented technique used to improve the performance of data access is Caching. Cooperative caching, which allows the sharing and coordination of cached data among multiple nodes, can further explore the potential of the caching techniques. Due to mobility and resource constraints of ad-hoc networks, cooperative caching techniques designed for wired network may not be applicable to ad-hoc networks. Hence, this paper presents a asymmetric cooperative caching scheme to efficiently support data access in ad-hoc networks. A Hybrid approach (Hybrid Cache) which can further improve the performance by taking advantage of Cache Data and Cache Path by avoiding general weaknesses. This proposed scheme increases the system performance in aspect of bandwidth, power utilization and end-end delay.
Sentiment analysis approach to adapt a shallow parsing based sentiment lexicon

With the rapid growing of IT development and e-commerce web sites, increasing trends in people to posting online reviews. Sentiment lexicons has offend used to analyzing the large volume of online review data available and gain useful knowledge from it. Most of the sentiment lexicon are aspect base, uses dependence parsing for extracting the word which are not be able to classify the sentimental word so accurately. Try to propose a method which combines sentiment lexicon and shallow parsing. Which determine aspect and domain base sentiment analysis and then assign polarity to a lexicon. Main merits of proposed methods is that it highly accurate and automatically generating structured to avoiding the cost of manually labelling data. The shallow parsing used to analyses sentence and get the constituents words. It will not considering the internal structure of constituent word, nor specifying their value in sentence. Then using polarity of words positive or negative evolution of the product conclude.
Interactive exploration of RNA22 microRNA target predictions

MicroRNA (miRNA) target prediction is an important problem. Given an miRNA sequence the task is to determine the identity of the messenger RNAs targeted by it, the locations within them where the interactions happen and the specifics of the formed heteroduplexes. Here, we describe a web-based application, RNA22-GUI, which we have designed and implemented for the interactive exploration and in-context visualization of predictions by RNA22, one of the popular miRNA target prediction algorithms. Central to our design has been the requirement to provide informative and comprehensive visualization that is integrated with interactive search capabilities and permits one to selectively isolate and focus on relevant information that is distilled on-the-fly from a large repository of pre-compiled predictions. RNA22-GUI is currently available for Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans.
About Subsumption in Fuzzy EL

Classical Description Logics (DLs) [2] cannot properly deal with the endemic imprecision of biomedical knowledge. For example, the current version of the SNOMEDCT ontology defines a “Perinatal Cyanotic Attack” as a cardiovascular disorder occurring in the perinatal period and manifested through cyanosis. This definition depends on two vague notions, namely the perinatal period—the period of time around birth—and cyanosis—a bluish discoloration of the skin. While it is possible to say that one year after birth is not perinatal, and a few hours from birth is, there is no precise threshold on the end of the perinatal period. However, it makes sense to say that every child is less in its perinatal period as time goes by. A similar consideration can be made for skin turning from red to blue in cases of cyanosis. The use of several degrees of truth has been proposed for dealing with these gradual changes, as well as other kinds of imprecisions. Mathematical Fuzzy Logic [12] generalizes classical logic by allowing real numbers from the interval [0, 1] to act as truth degrees. It allows to express, e.g. that a newborn child is in the perinatal period with degree 1, but a threeweek-old belongs to this period only with degree 0.3. In Mathematical Fuzzy Logic, the interpretation of the logical constructors, such as conjunction, disjunction, and implication, is determined by the choice of a binary triangular norm (or t-norm). Fuzzy Description Logics combine DLs with Mathematical Fuzzy Logic as a means to formally represent and reason with vague conceptual knowledge [18,19]. So far, research on fuzzy DLs was mainly focused on fuzzy extensions of propositionally closed DLs. Unfortunately, in fuzzy DLs a negation constructor often leads to undecidability [7,11]. To the best of our knowledge, the only fuzzy extensions of EL studied so far are based on the Godel t-norm [16,20]. In these logics, fuzzy subsumption between concepts can be decided in polynomial time. Beyond this tractable case, very little is known about the complexity of subsumption with general t-norms. If we restrict the set of membership degrees to be finite, subsumption can be decided in exponential time [3,8], but for the interval [0, 1] nothing is known, even for expressive fuzzy DLs in which consistency is decidable [5].
Scoring anomalies: a M-estimation formulation

It is the purpose of this paper to formulate the issue of scoring multivariate observations depending on their degree of abnormality/novelty as an unsupervised learning task. Whereas in the 1-d situation, this problem can be dealt with by means of tail estimation techniques, observations being viewed as all the more ”abnormal” as they are located far in the tail(s) of the underlying probability distribution. In a wide variety of applications, it is desirable to dispose of a scalar valued ”scoring” function allowing for comparing the degree of abnormality of multivariate observations. Here we formulate the issue of scoring anomalies as a M -estimation problem. A (functional) performance criterion is proposed, whose optimal elements are, as expected, nondecreasing transforms of the density. The question of empirical estimation of this criterion is tackled and preliminary statistical results related to the accuracy of partition-based techniques for optimizing empirical estimates of the empirical performance measure are established.
Research on knowledge practices with the contextual activity sampling system

The Contextual Activity Sampling System (CASS) research methodology and the CASS-Query application have been developed for contextually tracking of activities with a mobile phone. The method relies on frequent sampling of participants' practices and affects during periods of intensive follow-up. Two research designs provide an account of the methodological development work and the possibilities offered by CASS. The first study followed five student-groups longitudinally to examine evolution of academic knowledge practices. The findings from the second year data-collection show that trialogical practices were considered challenging, but often generated optimal-flow experiences. The second study investigated interprofessional work during a clinical course. Based on this pilot study, it was concluded that the data collected about activities and experiences over time extend the understanding of students' practices beyond what can be acquired by post-course questionnaires and can help in development of the design of interprofessional education in medicine and healthcare.
Students’ Attitudes towards Vocational Foreign Language Course

The aim of the study was to determine students’ attitudes towards Vocational Foreign Language Course and if the their attitudes display significant differences in terms of gender, age, department, the place they live, passing marks, the type of high school they graduated from, their mothers’ and fathers’ graduation levels and being abroad. The study was carried out in descriptive survey method. The population of the study comprised of senior students at two vocational colleges of Nevsehir Haci Bektas Veli University in 2015-2016 spring semester. “Attitude Scale towards Vocational Foreign Language Course” was used to collect data. Data were analyzed using independent samples t-test and one-way ANOVA. The findings revealed that students, in general, have positive attitudes towards Vocational Foreign Language Course and their attitudes differed in terms of gender, age, department and passing mark; however, their attitudes did not have a difference in terms of other variables.
Extraction Studies of Uranium(VI), Plutonium(IV) and Americium(III) from Nitric Acid Using the Bi-functional Carbamoyl Methyl Sulfoxide Ligands

The extraction behavior of new bi-functional ligands containing sulfoxide and amide groups viz . N , N ′-dibutyl carbamoyl methyl phenyl sulfoxide (L1) and N , N ′-dibutyl carbamoyl methyl benzyl sulfoxide (L2) towards the U(VI), Pu(IV) and Am(III) ions from nitric acid was studied. Both of these extractants showed appreciable extractions for U(VI) and Pu(IV) from 1 to 9.5 M nitric acid concentrations. Am(III) did not show an appreciable extraction under the conditions studied. The species extracted from a nitric acid medium correspond to the compositions of [UO_2(NO_3)_2•2L] and [Pu(NO_3)_4•2L] for L1 and a mixture of [UO_2(NO_3)_2•2L], [UO_2(NO_3)_2•L] and [Pu(NO_3)_4•2L] for the L2. The conditional extraction constant ( K _ex) values for the Pu(IV) with L1 and L2 were estimated for the first time, and found to be 6.21 × 10^2 and 5.64 × 10^2 mol^–4 dm, respectively.
G-CSF regulates macrophage phenotype and associates with poor overall survival in human triple-negative breast cancer

ABSTRACT Tumor-associated macrophages (TAMs) have been implicated in the promotion of breast cancer growth and metastasis, and a strong infiltration by TAMs has been associated with estrogen receptor (ER)-negative tumors and poor prognosis. However, the molecular mechanisms behind these observations are unclear. We investigated macrophage activation in response to co-culture with several breast cancer cell lines (T47D, MCF-7, BT-474, SKBR-3, Cal-51 and MDA-MB-231) and found that high granulocyte colony-stimulating factor (G-CSF) secretion by the triple-negative breast cancer (TNBC) cell line MDA-MB-231 gave rise to immunosuppressive HLA-DRlo macrophages that promoted migration of breast cancer cells via secretion of TGF-α. In human breast cancer samples (n = 548), G-CSF was highly expressed in TNBC (p < 0.001) and associated with CD163+ macrophages (p < 0.0001), poorer overall survival (OS) (p = 0.021) and significantly increased numbers of TGF-α+ cells. While G-CSF blockade in the 4T1 mammary tumor model promoted maturation of MHCIIhi blood monocytes and TAMs and significantly reduced lung metastasis, anti-CSF-1R treatment promoted MHCIIloF4/80hiMRhi anti-inflammatory TAMs and enhanced lung metastasis in the presence of high G-CSF levels. Combined anti-G-CSF and anti-CSF-1R therapy significantly increased lymph node metastases, possibly via depletion of the so-called “gate-keeper” subcapsular sinus macrophages. These results indicate that G-CSF promotes the anti-inflammatory phenotype of tumor-induced macrophages when CSF-1R is inhibited and therefore caution against the use of M-CSF/CSF-1R targeting agents in tumors with high G-CSF expression.
A Flexible Model of HIV-1 Latency Permitting Evaluation of Many Primary CD4 T-Cell Reservoirs

Latently infected cells form the major obstacle to HIV eradication. Studies of HIV latency have been generally hindered by the lack of a robust and rapidly deployable cell model that involves primary human CD4 T lymphocytes. Latently infected cell lines have proven useful, but it is unclear how closely these proliferating cells recapitulate the conditions of viral latency in non-dividing CD4 T lymphocytes in vivo. Current primary lymphocyte models more closely reflect the in vivo state of HIV latency, but they are limited by protracted culture periods and often low cell yields. Additionally, these models are always established in a single latently infected cell type that may not reflect the heterogeneous nature of the latent reservoir. Here we describe a rapid, sensitive, and quantitative primary cell model of HIV-1 latency with replication competent proviruses and multiple reporters to enhance the flexibility of the system. In this model, post-integration HIV-1 latency can be established in all populations of CD4 T cells, and reactivation of latent provirus assessed within 7 days. The kinetics and magnitude of reactivation were evaluated after stimulation with various cytokines, small molecules, and T-cell receptor agonists. Reactivation of latent HIV proviruses was readily detected in the presence of strong activators of NF-κB. Latently infected transitional memory CD4 T cells proved more responsive to these T-cell activators than latently infected central memory cells. These findings reveal potentially important biological differences within the latently infected pool of memory CD4 T cells and describe a flexible primary CD4 T-cell system to evaluate novel antagonists of HIV latency.
Eradication of hospital-acquired venous thromboembolism

Pulmonary embolism (PE) causes nearly 200,000 deaths annually in the United States alone. The magnitude of the risk for acquiring venous thromboembolism (VTE) in U.S. hospitals is staggering (1). About 8 million Medical Service and 4 million Surgical Service patients are at moderate or high risk for developing VTE each year (2). The surgeon General has declared that PE is the most preventable cause of death within hospitals (3). Thus, a spotlight shines brightly on quality control and quality improvement practices within American hospitals (4) to ensure that maximum effort is exerted to prevent PE and deep venous thrombosis (DVT). A convergence of passionate advocates (5), including health care providers, patients, and governmental authorities, will transform the status quo and enable eradication of hospital-acquired VTE. Catalysts for VTE eradication are listed in Table 1. Failure to prevent in-hospital PE and DVT will no longer be tolerated. For example, Medicare and Medicaid will have stopped reimbursing hospitals for incremental care needed to treat postoperative total hip or knee replacement patients who develop VTE (6). Whether this new policy is wise or equitable is debatable (7), but its influence in augmenting VTE prophylaxis and in decreasing the rate of postoperative VTE is undeniable. We have entered a new era that focuses on venous disease. This contemporary heightened awareness to VTE prevention constitutes a remarkable achievement. Only a decade ago, VTE was an orphan disease which received only a modicum of attention from major cardiology, pulmonary, and haematology specialty societies. Major organisations representing these specialties were concerned about VTE but did not embrace the field as a top priority. Transformative champions who had argued in favour of paying more attention to preventing venous thrombosis had to compete with more forceful voices that favoured emphasis on more traditional core subject matter for each organisation. Examples are acute coronary syndrome for cardiologists, asthma/chronic lung disease for pulmonologists, and leukaemia/lymphoma for haematologists. Venous disease education tended to be handled as an “afterthought. ” Discussion of VTE’s wide scope and potential for harm did not capture the imagination of professionals or the public. Apathy was a common response when the subject of VTE was raised. There was no unifying push toward universal protection of hospitalised patients against DVT and PE.
An AdS_3 Dual for Minimal Model CFTs

We propose a duality between the 2d W{sub N} minimal models in the large N't Hooft limit, and a family of higher spin theories on AdS{sub 3}. The 2d conformal field theories (CFTs) can be described as Wess-Zumino-Witten coset models, and include, for N=2, the usual Virasoro unitary series. The dual bulk theory contains, in addition to the massless higher spin fields, two complex scalars (of equal mass). The mass is directly related to the 't Hooft coupling constant of the dual CFT. We give convincing evidence that the spectra of the two theories match precisely for all values of the 't Hooft coupling. We also show that the renormalization group flows in the 2d CFT agree exactly with the usual AdS/CFT prediction of the gravity theory. Our proposal is in many ways analogous to the Klebanov-Polyakov conjecture for an AdS{sub 4} dual for the singlet sector of large N vector models.
Influences on help-seeking pathways among people with chronic illness and disease in a rural South African community

The study sought to explore influences on help-seeking pathways followed by patients with chronic illness and disease (CID) in a rural community of the Limpopo Province, South Africa. The sample consisted of ten people with CID (female = 6; age range 42 to 96 years; sugar diabetes = 50%, and high blood pressure = 30%). The participants responded to semi-structured interviews pertaining to the influences on their choices for help-seeking pathways. The data were analysed applying Interpretative Phenomenological Analysis (IPA). Prevailing influences on help-seeking pathways with CID included presumed cause of the illness, diagnosis agent and family process, nature of preferred treatment modality, and openness to alternative and complementary medicine.
Embedded infrared imaging to measure the deformation of a soft robotic actuator

Soft machine tables are industrial robots with a soft, computer-controlled, deformable surface. They are designed to manipulate objects placed on the surface by changing the surface shape. The current control approaches for the soft actuators embedded in the surface layer are open-loop, because appropriate sensors have not been developed, yet. In this report, we propose a solution based on an array of infrared sensors embedded in the soft actuator. For an existing soft machine table, we propose a sensor setup to measure the surface deformation from within a pneumatic chamber. The approach is supported by quantitative, experimental results. First, we prove the validity of the physical sensor principle. Secondly, we show that the sensor is operable under the constraints given by the design of the existing soft machine table.
Influence of coral and algal exudates on microbially mediated reef metabolism

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo‘orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.