Miracle-dz/UniFAR-FTUs huggingface dataset:
A Review and Appraisal of Deconvolution Methods to Evaluate in vivo Neuroendocrine Secretory Events

The scientific discipline of ncurocndocrinology has witncsscd the emergence of various new technologies in the last decade. For example, among such developments are molecular biological probes of neuroendocrine gene expression, quantitative neurophysiological techniques, advances in structural and morphological analyses, and thc application of mathematical and physical models to help elucidate the mechanistic basis of neuroendocrine phenomena. In the latter category, convolution modeling or deconvolution analysis provides one particular informative tool to describe quantitatively underlying neurobiological signals and in somc circumstances estimate simultaneously the secretion as well as the elimination kinetics of the event. In the simplest circumstance, measurements are made of hormone, metabolite, or substrate concentrations within a particular compartment (e.g. blood, cerebrospinal fluid) at frequent intervals over time. Then, if a priori knowledge of the effector’s disappearance rate from the system is available, pertinent calculations can be carried out to determine the magnitude of the secretory process. Alternatively, independent knowledge of the secretory function would allow one to assess the specific elimination kinetics from the effector concentrations over time. In a more demanding form, deconvolution analysis can be used to estimate both the secretion and elimination functions simultaneously from the observed data, if assumptions about the specific structure of the phenomena (e.g. the particular nature of the secretion event) are allowed. These concepts are illustrated in Fig. 1. The intent of the present review is to illustrate applications of deconvolution methods to neuroendocrinology. Consequently, a detailed mathematical treatment is not appropriate here, but can be obtained by the interested reader from relevant references given.
A Reliable Communication Model based on IEEE802.15.4 for WSANs in Smart Grids

Creating cyber-physical systems (CPSs) based on wireless sensor and actuator networks (WSANs) has great potential to improve the performance of Smart Grid. In addition, IEEE802.15. 4 has widely been regarded as an appropriate standard for WSANs, due to some striking and unique features. WSANs require provisioning strict quality of service (QoS) due to noisy harsh environments in Smart Grid applications. Although analytical models have been studied in the literature, they have not provided a full-fledged model for Smart Grid. In this paper, we have added a MAC-level buffer, and a novel Markov chain model has been also proposed. By comparison with previous studies, retransmission confines, acknowledgment, packet length variation, saturated traffic, and degenerate distribution of packet generation are accounted for. The algorithm has been experimentally implemented and appraised on a platform with self-designed WSAN. The analytical model predicts well our exhaustive experiments. Further, Monte Carlo simulations validate mathematical results.
Image Denoising with Kernels Based on Natural Image Relations

A successful class of image denoising methods is based on Bayesian approaches working in wavelet representations. The performance of these methods improves when relations among the local frequency coefficients are explicitly included. However, in these techniques, analytical estimates can be obtained only for particular combinations of analytical models of signal and noise, thus precluding its straightforward extension to deal with other arbitrary noise sources. In this paper, we propose an alternative non-explicit way to take into account the relations among natural image wavelet coefficients for denoising: we use support vector regression (SVR) in the wavelet domain to enforce these relations in the estimated signal. Since relations among the coefficients are specific to the signal, the regularization property of SVR is exploited to remove the noise, which does not share this feature. The specific signal relations are encoded in an anisotropic kernel obtained from mutual information measures computed on a representative image database. In the proposed scheme, training considers minimizing the Kullback-Leibler divergence (KLD) between the estimated and actual probability functions (or histograms) of signal and noise in order to enforce similarity up to the higher (computationally estimable) order. Due to its non-parametric nature, the method can eventually cope with different noise sources without the need of an explicit re-formulation, as it is strictly necessary under parametric Bayesian formalisms. Results under several noise levels and noise sources show that: (1) the proposed method outperforms conventional wavelet methods that assume coefficient independence, (2) it is similar to state-of-the-art methods that do explicitly include these relations when the noise source is Gaussian, and (3) it gives better numerical and visual performance when more complex, realistic noise sources are considered. Therefore, the proposed machine learning approach can be seen as a more flexible (model-free) alternative to the explicit description of wavelet coefficient relations for image denoising.
Novel Approaches for Predicting Risk Factors of Atherosclerosis

Coronary heart disease (CHD) caused by hardening of artery walls due to cholesterol known as atherosclerosis is responsible for large number of deaths worldwide. The disease progression is slow, asymptomatic, and may lead to sudden cardiac arrest, stroke, or myocardial infraction. Presently, imaging techniques are being employed to understand the molecular and metabolic activity of atherosclerotic plaques to estimate the risk. Though imaging methods are able to provide some information on plaque metabolism, they lack the required resolution and sensitivity for detection. In this paper, we consider the clinical observations and habits of individuals for predicting the risk factors of CHD. The identification of risk factors helps in stratifying patients for further intensive tests such as nuclear imaging or coronary angiography. We present a novel approach for predicting the risk factors of atherosclerosis with an in-built imputation algorithm and particle swarm optimization (PSO). We compare the performance of our methodology with other machine-learning techniques on STULONG dataset which is based on longitudinal study of middle-aged individuals lasting for 20 years. Our methodology powered by PSO search has identified physical inactivity as one of the risk factors for the onset of atherosclerosis in addition to other already known factors. The decision rules extracted by our methodology are able to predict the risk factors with an accuracy of 99.73% which are higher than the accuracies obtained by the application of the state-of-the-art machine-learning techniques presently being employed in the identification of atherosclerosis risk studies.
ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl. ch/software.html.
Identification of an Intracellular Site of Prion Conversion

Prion diseases are fatal, neurodegenerative disorders in humans and animals and are characterized by the accumulation of an abnormally folded isoform of the cellular prion protein (PrPC), denoted PrPSc, which represents the major component of infectious scrapie prions. Characterization of the mechanism of conversion of PrPC into PrPSc and identification of the intracellular site where it occurs are among the most important questions in prion biology. Despite numerous efforts, both of these questions remain unsolved. We have quantitatively analyzed the distribution of PrPC and PrPSc and measured PrPSc levels in different infected neuronal cell lines in which protein trafficking has been selectively impaired. Our data exclude roles for both early and late endosomes and identify the endosomal recycling compartment as the likely site of prion conversion. These findings represent a fundamental step towards understanding the cellular mechanism of prion conversion and will allow the development of new therapeutic approaches for prion diseases.
EphA4-Mediated Ipsilateral Corticospinal Tract Misprojections Are Necessary for Bilateral Voluntary Movements But Not Bilateral Stereotypic Locomotion

In this study, we took advantage of the reported role of EphA4 in determining the contralateral spinal projection of the corticospinal tract (CST) to investigate the effects of ipsilateral misprojections on voluntary movements and stereotypic locomotion. Null EphA4 mutations produce robust ipsilateral CST misprojections, resulting in bilateral corticospinal tracts. We hypothesize that a unilateral voluntary limb movement, not a stereotypic locomotor movement, will become a bilateral movement in EphA4 knock-out mice with a bilateral CST. However, in EphA4 full knock-outs, spinal interneurons also develop bilateral misprojections. Aberrant bilateral spinal circuits could thus transform unilateral corticospinal control signals into bilateral movements. We therefore studied mice with conditional forebrain deletion of the EphA4 gene under control by Emx1, a gene expressed in the forebrain that affects the developing CST but spares brainstem motor pathways and spinal motor circuits. We examined two conditional knock-outs targeting forebrain EphA4 during performance of stereotypic locomotion and voluntary movement: adaptive locomotion over obstacles and exploratory reaching. We found that the conditional knock-outs used alternate stepping, not hopping, during overground locomotion, suggesting normal central pattern generator function and supporting our hypothesis of minimal CST involvement in the moment-to-moment control of stereotypic locomotion. In contrast, the conditional knock-outs showed bilateral voluntary movements under conditions when single limb movements are normally produced and, as a basis for this aberrant control, developed a bilateral motor map in motor cortex that is driven by the aberrant ipsilateral CST misprojections. Therefore, a specific change in CST connectivity is associated with and explains a change in voluntary movement.
Congestion Control and Sizing Router Buffers in the Internet

The Internet is made of communication links and packet switching nodes named routers. Routers are equipped with buffers that hold packets during congestion and feed output links with packets during underutilization. A rule largely known in literature is the "bandwidth-delay rule", which states that, in order to guarantee full link utilization, it is necessary to provide each link with a buffer B = RTT.C, where RTT is the round trip time and C is the link capacity. The bandwidth delay rule requires buffer size that increases linearly with link capacity. With the recent introduction of 10 Gbps Routers and Ethernet cards, buffer requirements as dictated by the bandwidth-delay rule become extremely large. For instance, a 10Gbps router link with a RTT of 200ms would require a 2Gbits buffer size, which is a challenging requirement for manufacturers. Moreover, such a large buffers would introduce large and time-varying queuing delays that are harmful for time sensitivity traffic such as audio and video. In this paper we investigate the relation between the TCP congestion control and the buffer size required to guarantee full link utilization. We consider two TCP congestion control algorithms: the standard TCP NewReno and the recently proposed TCP Westwood+. Analytical results show that while classic TCP Reno/NewReno requires buffer of order size ~ 1 n, where n is the number of coexisting flows, Westwood+ TCP, in principle, can provide full link utilization for any buffer size.
Epidemiology of primary hyperparathyroidism

The impact of primary hyperparathyroidism (HPT) on the population has not been well documented, and even less information is available for asymptomatic HPT. Only 57 deaths were attributed to the condition in the United States in 1986, for a reported HPT death rate of 0.24 per million per year. Many more patients were affected, however, and the incidence of hospitalization for HPT was 6.6 per 100,000 in 1986, counting all listed diagnoses, and 2.9 per 100,000 counting only first‐listed diagnoses. Surgery was performed on approximately 10,000 hospitalized patients in the United States in 1986, for a parathyroidectomy rate of about 4.2 per 100,000 per year. When nonhospitalized cases are included, the rates are even higher. The estimated annual incidence of HPT was 42.1 per 100,000 in Rochester, Minnesota in 1974–1976; the prevalence of HPT was 4.3 per 1000 in a population survey in Sweden. By any of these measures, HPT is more common in women than men and increases with aging in both sexes. The potential cost of HPT could be as high as $420 million/year in the United States, but no formal estimates have been made. Disability related to HPT or its treatment has not been quantified; randomized clinical trials to determine the utility of parathyroidectomy have not been performed; and no assessment of cost benefit or cost effectiveness of any therapeutic modality has been carried out. Until patient management and cost issues are resolved, it is premature to consider an aggressive program to screen the general population for HPT.
Why is Partial-breast Irradiation Still Investigational

The investigational nature of partial breast irradiation (PBI) remains an area of controversy in the field of breast radiotherapy. While we have a long track record of conducting and strongly supporting the research in this area, we have chosen the more cautious approach of continuing to offer PBI only as part of a trial, open to selected breast cancer patients at low risk of local recurrence. This position reflects the fact that existing whole breast radiotherapy has revealed very successful in controlling local recurrences and it remains the safest choice for the patient. Our thinking has been reinforced by the recent data linking the prevention of recurrence to long term breast cancer survival: until more is known about PBI safety, its indiscriminate use may deprive some women from their best chance of fighting breast cancer. Considerations regarding the correct interpretation of the available evidence in view of the still limited duration of follow up and of the pattern of local recurrence of breast cancer sustain our position that PBI can be offered only in the context of a clinical trial. Unfortunately, more time and data are warranted for PBI to be legitimately recognized a standard radiotherapy approach in breast conservation therapy.
Cardiac Raptor Ablation Impairs Adaptive Hypertrophy, Alters Metabolic Gene Expression, and Causes Heart Failure in Mice

Background— Cardiac hypertrophy involves growth responses to a variety of stimuli triggered by increased workload. It is an independent risk factor for heart failure and sudden death. Mammalian target of rapamycin (mTOR) plays a key role in cellular growth responses by integrating growth factor and energy status signals. It is found in 2 structurally and functionally distinct multiprotein complexes called mTOR complex (mTORC) 1 and mTORC2. The role of each of these branches of mTOR signaling in the adult heart is currently unknown. Methods and Results— We generated mice with deficient myocardial mTORC1 activity by targeted ablation of raptor, which encodes an essential component of mTORC1, during adulthood. At 3 weeks after the deletion, atrial and brain natriuretic peptides and &bgr;-myosin heavy chain were strongly induced, multiple genes involved in the regulation of energy metabolism were altered, but cardiac function was normal. Function deteriorated rapidly afterward, resulting in dilated cardiomyopathy and high mortality within 6 weeks. Aortic banding–induced pathological overload resulted in severe dilated cardiomyopathy already at 1 week without a prior phase of adaptive hypertrophy. The mechanism involved a lack of adaptive cardiomyocyte growth via blunted protein synthesis capacity, as supported by reduced phosphorylation of ribosomal S6 kinase 1 and 4E-binding protein 1. In addition, reduced mitochondrial content, a shift in metabolic substrate use, and increased apoptosis and autophagy were observed. Conclusions— Our results demonstrate an essential function for mTORC1 in the heart under physiological and pathological conditions and are relevant for the understanding of disease states in which the insulin/insulin-like growth factor signaling axis is affected such as diabetes mellitus and heart failure or after cancer therapy.
HIS-24 Linker Histone and SIR-2.1 Deacetylase Induce H3K27me3 in the Caenorhabditis elegans Germ Line

ABSTRACT HIS-24 linker histone and SIR-2.1 deacetylase are involved in chromatin silencing in Caenorhabditis elegans. Depletion of SIR-2.1 results in cytoplasmic retention of HIS-24 in oocytes. However, the molecular working mechanisms of HIS-24 and SIR-2.1 are unclear. We show here a synergistic function of SIR-2.1 and HIS-24 that are together essential for maintenance of the H3K27me3 mark in the germ line of C. elegans. We demonstrate the synthetic effects of the two factors on brood size, embryogenesis, and fertility. SIR-2.1 and HIS-24 associate with the subtelomeric regions but apparently do not interact directly. We report that SIR-2.1 deacetylates H3K9 at subtelomeric regions and suggest that deacetylation of H3K9 is a prerequisite for H3K27 methylation. In turn, we found that HIS-24 specifically interacts with the histone H3 K27 region, when unmodified or in the trimethylated state. Overall, our data indicate that SIR-2.1 and HIS-24 contribute to the propagation of a specialized chromatin state at the subtelomeric regions and elsewhere in the genome.
Respiratory Tract Epithelial Cells Express Retinaldehyde Dehydrogenase ALDH1A and Enhance IgA Production by Stimulated B Cells in the Presence of Vitamin A

Morbidity and mortality due to viral infections are major health concerns, particularly when individuals are vitamin A deficient. Vitamin A deficiency significantly impairs mucosal IgA, a first line of defense against virus at its point of entry. Previous reports have suggested that CD11cHi dendritic cells (DCs) of the gastrointestinal tract produce retinaldehyde dehydrogenase (ALDH1A), which metabolizes vitamin A precursors to retinoic acid to support normal mucosal immunity. Given that the upper respiratory tract (URT) and gastrointestinal tract share numerous characteristics, we asked if the CD11cHi DCs of the URT might also express ALDH1A. To address this question, we examined both CD11cHi test cells and CD11cLo/neg control cells from nasal tissue. Surprisingly, the CD11cLo/neg cells expressed more ALDH1A mRNA per cell than did the CD11cHi cells. Further evaluation of CD11cLo/neg populations by PCR and staining of respiratory tract sections revealed that epithelial cells were robust producers of both ALDH1A mRNA and protein. Moreover, CD11cLo/neg cells from nasal tissue (and a homogeneous respiratory tract epithelial cell line) enhanced IgA production by lipopolysaccharide (LPS)-stimulated splenocyte cultures in the presence of the retinoic acid precursor retinol. Within co-cultures, there was increased expression of MCP-1, IL-6, and GM-CSF, the latter two of which were necessary for IgA upregulation. All three cytokines/chemokines were expressed by the LPS-stimulated respiratory tract epithelial cell line in the absence of splenocytes. These data demonstrate the autonomous potential of respiratory tract epithelial cells to support vitamin A-mediated IgA production, and encourage the clinical testing of intranasal vitamin A supplements in vitamin A deficient populations to improve mucosal immune responses toward respiratory tract pathogens and vaccines.
Variable frame rate video for mobile devices

In [1] we introduced a new real-time variable frame rate control scheme. It is based on the video jerkiness and it can be applied to both coding and transcoding. This scheme constantly traces the motion of the incoming video and automatically tunes the outgoing frame rate according to the level of jerkiness acceptable by the user. This scheme has been conceived in the framework of mobile communications, which calls for an optimum use of both the available bandwidth and terminal resources. In this paper we present a subjective assessment of our solution carried out in a professional laboratory suitably equipped. Towards this aim a group of non-expert users was asked to express their preference when watching side by side the same video coded at variable frame rate and at fixed frame rate. Results show that most of the times a variable frame rate control based on a dynamic bit/frame allocation scheme may substantially improve the video quality perceived by the users.