Miracle-dz/UniFAR-FTUs huggingface dataset:
Watersnakes: Energy-Driven Watershed Segmentation

The watershed algorithm from mathematical morphology is powerful for segmentation. However, it does not allow incorporation of a priori information as segmentation methods that are based on energy minimization. In particular, there is no control of the smoothness of the segmentation result. In this paper, we show how to represent watershed segmentation as an energy minimization problem using the distance-based definition of the watershed line. A priori considerations about smoothness can then be imposed by adding the contour length to the energy function. This leads to a new segmentation method called watersnakes, integrating the strengths of watershed segmentation and energy based segmentation. Experimental results show that, when the original watershed segmentation has noisy boundaries or wrong limbs attached to the object of interest, the proposed method overcomes those drawbacks and yields a better segmentation.
Boomerang: resourceful lenses for string data

A lens is a bidirectional program. When read from left toright, it denotes an ordinary function that maps inputs to outputs. When read from right to left, it denotes an ''update translator'' that takes an input together with an updated output and produces a new input that reflects the update. Many variants of this idea have been explored in the literature, but none deal fully with ordered data. If, for example, an update changes the order of a list in theoutput, the items in the output list and the chunks of the input that generated them can be misaligned, leading to lost or corrupted data. We attack this problem in the context of bidirectional transformations over strings, the primordial ordered data type. We first propose a collection of bidirectional string lens combinators, based on familiar operations on regular transducers (union, concatenation, Kleene-star) and with a type system based on regular expressions. We then design anew semantic space of dictionary lenses, enriching the lenses of Foster et al. (2007) with support for two additional combinators for marking ''reorderable chunks'' andtheir keys. To demonstrate the effectiveness of these primitives, we describe the design and implementation of Boomerang, a full-blown bidirectional programming language with dictionary lenses at its core. We have used Boomerang to build transformers for complex real-world data format sincluding the SwissProt genomic database. We formalize the essential property of resourcefulness-the correct use of keys to associate chunks in the input and output-by defining a refined semantic space of quasi-oblivious lenses. Several previously studied properties of lenses turn out to have compact characterizations in this space.
Front-line doublets in advanced non-small cell lung cancer: The golden age for second line chemotherapy.

A doublet chemotherapy, generally cisplatin or carboplatin-based, is the standard of care in the management of advanced non-small cell lung cancer (NSCLC) patients, defined as unre-sectable stage IIIB or stage IV disease [1]. Numerous trials have established the superiority of third generation cytotoxic agent combinations over old fashion regimens (2 –4). In one of these studies published by Bonomi et al., the classical eto-poside-cisplatin doublet (EC, etoposide 100 mg/m 2 days 1 to 3, plus cisplatin 75 mg/m 2 day 1) was compared with two different paclitaxel-cisplatin regimens (cisplatin 75 mg/m 2 plus paclitaxel 135 or 250 mg/m 2 as a 24-hour infusion) [3]. The median failure-free survival was 2.8 months for EC and 4.8 months in the paclitaxel arms, translating to a significant increase of median overall survival from 7.5 months to 9.9 months, respectively. Paclitaxel plus cisplatin was subsequently shown to be equivalent to the more convenient combination of paclitaxel and carboplatin (PC) which became the North-American reference regimen [5]. In this issue of Annals of Oncology, the phase III study reported by Belani et al. failed to detect the hypothesised 40% improvement in median survival comparing PC (carboplatin AUC = 6, paclitaxel 225 mg/m2) with EC (power of 85%, alpha of 0.05) as first line chemotherapy in 369 patients with advanced NSCLC [6]. Surprisingly, there is a trend for better median overall survival and one year survival rate in the EC arm (9.1 months and 37%) compared to the PC arm (7.7 months and 32%). The unexpected results of this trial may raise some concerns about the efficacy of the PC doublet, but also reflect a positive evolution in the medical management of advanced NSCLC. Median time to progression was similar in EC and PC arms (3.6 and 4 months, respectively, P = 0.877), taking into account that patients in the PC arm received more cycles than in the EC arm (median number of four cycles versus three, respectively) and had less dose reductions (percentage of planned dose not reported). Patient populations in both arms were well balanced except for gender (more females in the EC arm). Performance status and prior weight loss had a significant impact on OS, without interacting with study results since patients were stratified at enrolment on these two factors. No details on histological subtypes and their predictive value were provided. This might be of importance because recent data outlined that specific tumour …
Model Calcium Sensors for Network Homeostasis: Sensor and Readout Parameter Analysis from a Database of Model Neuronal Networks

In activity-dependent homeostatic regulation (ADHR) of neuronal and network properties, the intracellular Ca2+ concentration is a good candidate for sensing activity levels because it is correlated with the electrical activity of the cell. Previous ADHR models, developed with abstract activity sensors for model pyloric neurons and networks of the crustacean stomatogastric ganglion, showed that functional activity can be maintained by a regulation mechanism that senses activity levels solely from Ca2+. At the same time, several intracellular pathways have been discovered for Ca2+-dependent regulation of ion channels. To generate testable predictions for dynamics of these signaling pathways, we undertook a parameter study of model Ca2+ sensors across thousands of model pyloric networks. We found that an optimal regulation signal can be generated for 86% of model networks with a sensing mechanism that activates with a time constant of 1 ms and that inactivates within 1 s. The sensor performed robustly around this optimal point and did not need to be specific to the role of the cell. When multiple sensors with different time constants were used, coverage extended to 88% of the networks. Without changing the sensors, it extended to 95% of the networks by letting the sensors affect the readout nonlinearly. Specific to this pyloric network model, the sensor of the follower pyloric constrictor cell was more informative than the pacemaker anterior burster cell for producing a regulatory signal. Conversely, a global signal indicating network activity that was generated by summing the sensors in individual cells was less informative for regulation.
Superconcentrators, generalizers and generalized connectors with limited depth

We show that the minimum possible size of an n-superconcentrator with depth 2k≥4 is θ(nλ(k, n)), where λ(k, .) is the inverse of a certain function at the k-th level of the primitive recursive hierarchy. It follows that the minimum possible depth of an n-superconcentrator with linear size is θ(β(n)), where β is the inverse of a function growing more rapidly than any primitive recursive function. Similar results hold for generalizers. We give a simple explicit construction for a (d1.dk)-generalizer with depth k and size (d1+.+dk)d1.dk. This is applied to give a simple explicit construction for a generalized n-connector with depth 2k−3 and size (2d1+3d2+.+3dk−1+2dk) d1.dk. These are the best explicit constructions currently available. We also show that, for each fixed k≥2, the minimum possible size of a generalized n-connector with depth k is Ω(n1+1/k) and 0((n log n)1+1/k).
Mechanisms of regulation of cell-mediated immunity. III. The characterization of azobenzenearsonate-specific suppressor T-cell- derived-suppressor factors

Delayed type hypersensitivity to the hapten azobenzenearsonate (ABA) can be induced and suppressed by the administration of hapten-coupled syngeneic spleen cells by the appropriate route. Suppressor T cells stimulated by the intravenous administration of ABA-coupled spleen cells have been shown to produce a discrete subcellular factor(s) which is capable of suppressing delayed type hypersensitivity to azobenzenearsonate in the mouse. Such suppressor factors may be produced by the mechanical disruption of suppressor cells or by placing such suppressor cells in culture for 24 h. The suppressor factor(s) (SF) derived from ABA-specific suppressor cells exhibit biological specificity for the suppression of ABA delayed type hypersensitivity (DTH), but not trinitro-phenyl DTH, as well as the capacity to bind to ABA immunoadsorbents. Passage of suppressor factor(s) over reverse immunoadsorbents utilizing a rabbit anti-mouse F(ab')2 antiserum demonstrated that the antigen-specific T-cell derived SF does not bear conventional immunoglobulin markers. The suppressor factor(s) are not immunoglobulin molecules was further demonstrated by the inability of anti-ABA antibodies to suppress ABA DTH. Gel filtration of ABA suppressor factor(s) showed that the majority of the suppressive activity was present in a fraction with molecular weight ranging between 6.8 x 10(4) and 3.3 x 10(4) daltons. We also analyzed for the presence of determinants encoded by the H-2 major histocompatibility complex (MHC) and found that immunoadsorbents prepared utilizing antisera capable of interacting with gene products of the whole or selected gene regions of H-2 MHC, i.e., B10.D2 anti-B10.A and B10 anti- B10.A immunoadsorbents, retained the suppressive activity of ABA-SF. Elution of such columns with glycine HCl buffers (pH 2.8) permitted recovery of specific suppressive activity. Taken collectively such data supports the notion that suppressor T-cell-derived ABA suppressor factors have antigen-binding specificity as well as determinants controlled by the K end of the H-2 MHC. The distribution of strains capable of making SF has also been analyzed. The relationship of the antigen-binding specificity to VH gene products is discussed in this and the companion paper.
Diagnostic value of serum precipitins to mould antigens in active hypersensitivity pneumonitis

Serum precipitins have a controversial diagnostic value in hypersensitivity pneumonitis (HP). The present authors’ objective was to assess their diagnostic value by developing scores from a panel of specific antigens tested by two techniques (electrosyneresis and double diffusion) to discriminate active HP from other interstitial lung diseases. Consecutive patients presenting with a condition for which HP was considered in the differential diagnosis were included in the study. All patients underwent the same standardised diagnostic procedure, including precipitin tests performed in routine conditions. Clinical manifestations, bronchoalveolar lavage and high-resolution computed tomography defined the presence or absence of HP. Receiver-operating characteristic curves and logistic regression were used to develop the serological scores. A total of 122 patients (including 31 cases of HP) were included in the study. Five antigens from the panel were selected for the serological scores (Absidia corymbifera, Eurotium amstelodami, Wallemia sebi, Saccharopolyspora rectivirgula and mesophilic Streptomyces sp.). Electrosyneresis was more discriminative than the double-diffusion technique. Predictive negative values varied 81–88% and predictive positive values varied 71–75% for prevalence of HP 20–35%. In conclusion, serological scores using a panel of relevant antigens may guide both biological and clinical practice in areas of high prevalence of hypersensitivity pneumonitis.
One-dimensional multi-subband Monte Carlo simulation of charge transport in Si nanowire transistors

In this paper, we employ a newly-developed one-dimensional multi-subband Monte Carlo (1DMSMC) simulation module to study electron transport in nanowire structures. The 1DMSMC simulation module is integrated into the GSS TCAD simulator GARAND coupling a MC electron trajectory simulation with a 3D Poisson-2D Schrödinger solver, and accounting for the modified acoustic phonon, optical phonon, and surface roughness scattering mechanisms. We apply the simulator to investigate the effect of the overlap factor, scattering mechanisms, material and geometrical properties on the mobility in silicon nanowire field-effect transistors (NWTs). This paper emphasizes the importance of using 1D models that include correctly quantum confinement and allow for a reliable prediction of the performance of NWTs at the scaling limits. Our simulator is a valuable tool for providing optimal designs for ultra-scaled NWTs, in terms of performance and reliability.
Cholesterol Diet Withdrawal Leads to an Initial Plaque Instability and Subsequent Regression of Accelerated Iliac Artery Atherosclerosis in Rabbits

Effect of long term cholesterol diet withdrawal on accelerated atherosclerosis in iliac artery of New Zealand White (NZW) rabbits has not been explored so far. Atherosclerosis was thus induced in rabbits by a combination of balloon injury and atherogenic diet (AD) (1% cholesterol and 6% peanut oil) feeding for 8 weeks (baseline) followed by chow diet (CD) feeding for 4, 8, 16, 32, 50 and 64 weeks. The plaque characterization was done using histology, real time RT-PCR and vasoreactivity studies. Significant elevation in plasma lipids with AD feeding was normalized following 16 weeks of CD feeding. However, baseline comparison showed advanced plaque features even after 8 weeks of CD period with significant elevation in intima/media thickness ratio and plaque area later showing reduction at 50 and 64 weeks CD periods. Lesion lipid accumulation and CD68 positivity was maintained till 16 weeks of CD feeding which significantly reduced from 32 to 64 weeks CD periods. Baseline comparison showed significant increase in ground substance, MMP-9 and significant decrease in α-actin and collagen content at 8 weeks CD period indicating features of unstable plaque. These features regressed up to 64 weeks of CD. Partial restoration of functional vasoconstriction and vasorelaxation was seen after 64 weeks of CD feeding. mRNA expression of MCP-1, VCAM-1, collagen type I and III, MMP-9, TIMP-1, IFN-γ, TNF-α, IL-10 and eNOS supported the above findings. The study thus reveals insights into initial plaque instability and subsequent regression on AD withdrawal in this model. These results are suggestive of an appropriate window for drug intervention for plaque stability/regression and restenosis as well as improves understanding of plaque regression phenomenon in this model.
Localizing evoked and induced responses to faces using magnetoencephalography

A rich pattern of responses in frequency, time and space are known to be generated in the visual cortex in response to faces. Recently, a number of studies have used magnetoencephalography (MEG) to try to record these responses non‐invasively – in many cases using source analysis techniques based on the beamforming method. Here we sought both to characterize best practice for measuring face‐specific responses using MEG beamforming, and to determine whether the results produced by the beamformer match evidence from other modalities. We measured activity to visual presentation of face stimuli and phase‐scrambled control stimuli, and performed source analyses of both induced and evoked responses using Synthetic Aperture Magnetometry. We localized the gamma‐band response to bilateral lateral occipital cortex, and both the gamma‐band response and the M170‐evoked response to the right fusiform gyrus. Differences in the gamma‐band response between faces and scrambled stimuli were confined to the frequency range 50–90 Hz; gamma‐band activity at higher frequencies did not differ between the two stimulus categories. We additionally identified a component of the M220‐evoked response – localized to the parieto‐occipital sulcus – which was enhanced for scrambled vs. unscrambled faces. These findings help to establish that MEG beamforming can localize face‐specific responses in time, frequency and space with good accuracy (when validated against established findings from functional magnetic resonance imaging and intracranial recordings), as well as contributing to the establishment of best methodological practice for the use of the beamformer method to measure face‐specific responses.
Evidence that Climbing Fibers Control an Intrinsic Spike Generator in Cerebellar Purkinje Cells

It is well established that the climbing fiber (CF) input to a cerebellar Purkinje cell (PC) can exert a controlling influence on the background simple spike (SS) activity of the cell, in that repetitive stimulation of CFs causes a decrease in SS activity, and removal or inactivation of CFs is followed by a rise in activity. In the present study, the effects of inactivation of CFs in the short term and longer term (hours) were investigated in anesthetized rats to determine how the CFs control the PC SS activity. Inactivation of the CF input to a PC was accomplished by either reversibly inactivating with lignocaine or by microlesioning the inferior olive. Consistent with previous findings, CF removal caused a transformation of the PC firing pattern, with SSs discharging more regularly and rising to an exceptionally high level. In cases in which CF activity resumed, SS rate declined to control levels within a few seconds. However, with sustained CF inactivation (30 min to 5 hr), SS activity continues to rise progressively and develops an oscillating firing pattern, consisting of alternating bursts of high-frequency discharge at up to 100-150 Hz followed by 10-20 sec periods of electrical quiescence. No accompanying changes in the threshold for evoking SSs via the parallel fibers were seen to accompany the increases in tonic SS activity. We conclude that the increase in SS activity that follows CF inactivation could be caused by the removal of an inhibitory action that CFs exert on the intrinsic pacemaker present in PCs under normal conditions.
Voting-based depth map refinement and propagation for 2D to 3D conversion

In this paper, a voting-based filter which is capable of enhancing the quality of depth map sequence and interpolates missing frames is proposed. The main concept is that if the information in the filter window is not consistent, then only the multitude decides the output. The minority will be considered as outliers. Compare to other depth map refinement method using joint bilateral filter, the outlier detection of the proposed scheme ensures that only appropriate information is involved so that the halo effects can be avoided. Moreover, in order to refine a sequence of depth maps, a space-time filtering extension is proposed. This extension refines each depth map according to the information of several adjacent frames rather than only one frame. As a result, the proposed method is capable of interpolating missing depth maps of a sequence and the errors on the depth maps are successfully reduced. The experimental results demonstrate that the voting-based filter not only provides a depth map sequence with good quality and temporal consistency but also provides several post-processing for depth maps in 2D to 3D conversion due to its flexibility.
IFN Regulatory Factor 8 Is a Key Constitutive Determinant of the Morphological and Molecular Properties of Microglia in the CNS

IFN regulatory factor (IRF) 8 is a transcription factor that has a key role in the cellular response to IFN-γ and is pivotal in myeloid cell differentiation. Whether IRF8 plays a role in the development and function of microglia, the tissue-resident myeloid cells of the brain, is unknown. Here, we show IRF8 is a constitutively produced nuclear factor in microglia, which suggested that IRF8 might also be a key homeostatic transcriptional determinant of the microglial cell phenotype. In support of this, in mice with a targeted disruption of the IRF8 gene, microglia were increased in number and showed gross alterations in morphology and surface area. In situ analysis of some key myeloid markers revealed that IRF8-deficient microglia had significantly reduced levels of Iba1, but increased levels of CD206 (mannose receptor) and F4/80 as well as increased tomato lectin binding. Analysis of microglia ex vivo revealed IRF8-deficient microglia had significantly increased levels of CD45, CD11b and F4/80, but significantly decreased levels of the chemokine receptors CCR2, CCR5 and CX3CR1. The known involvement of some of these molecular markers in membrane dynamics and phagocytosis led us to examine the phagocytic capacity of cultured IRF8-deficient microglia, however, this was found to be similar to wild type microglia. We conclude IRF8 is a constitutively produced nuclear factor in resident microglia of the CNS being a crucial transcriptional determinant of the phenotype of these cells in the healthy brain.
Atmospheric-Pressure Cold Plasma Induces Transcriptional Changes in Ex Vivo Human Corneas

Background Atmospheric pressure cold plasma (APCP) might be considered a novel tool for tissue disinfection in medicine since the active chemical species produced by low plasma doses, generated by ionizing helium gas in air, induces reactive oxygen species (ROS) that kill microorganisms without substantially affecting human cells. Objectives In this study, we evaluated morphological and functional changes in human corneas exposed for 2 minutes (min) to APCP and tested if the antioxidant n-acetyl l-cysteine (NAC) was able to inhibit or prevent damage and cell death. Results Immunohistochemistry and western blotting analyses of corneal tissues collected at 6 hours (h) post-APCP treatment demonstrated no morphological tissue changes, but a transient increased expression of OGG1 glycosylase that returned to control levels in 24 h. Transcriptome sequencing and quantitative real time PCR performed on different corneas revealed in the treated corneas many differentially expressed genes: namely, 256 and 304 genes showing expression changes greater than ± 2 folds in the absence and presence of NAC, respectively. At 6 h post-treatment, the most over-expressed gene categories suggested an active or enhanced cell functioning, with only a minority of genes specifically concerning oxidative DNA damage and repair showing slight over-expression values (<2 folds). Moreover, time-related expression analysis of eight genes up-regulated in the APCP-treated corneas overall demonstrated the return to control expression levels after 24 h. Conclusions These findings of transient oxidative stress accompanied by wide-range transcriptome adjustments support the further development of APCP as an ocular disinfectant.
Change of Scale and Forecasting with the Control-Function Method in Logit Models

Endogeneity is a model misspecification that precludes the consistent estimation of the model parameters. The control-function method is the most suitable tool to address endogeneity for several discrete choice models that are relevant in transportation research. However, the estimators obtained with the control-function method are consistent only up to a scale. In this paper, we first depict the determinants of this change of scale by adapting an existing result for omitted orthogonal attributes in logit models. Then, we study the problem of forecasting under these circumstances. We show that a procedure proposed in previous literature may lead to significant biases, and we suggest novel alternatives to be used with synthetic populations. We use Monte Carlo experimentation and real data on residential location choice to illustrate these results. The paper finishes by summarizing the findings of this investigation and suggesting future lines of research in this area.