Miracle-dz/UniFAR-FTUs huggingface dataset:
Connectivity Re-establishment in the Presence of Dumb Nodes in Sensor-Cloud Infrastructure: A Game Theoretic Approach

In this work, we consider the presence of dumb nodes in the underlying physical networks of Sensor-Cloud infrastructure. The dumb nodes get isolated from the network and degrade the network performance. Consequently, a Cloud Service Provider (CSP) is unable to use Wireless Sensor Networks (WSNs) in an efficient manner, as the dumb sensor nodes cannot use as a virtual sensor. Thus, in this work, we propose a scheme, Connectivity Re-establishment in the Presence of Dumb Nodes in Sensor-Cloud Infrastructure (CoRDS), that facilitates the reestablishment of the connectivity between dumb nodes and the sink. Using the proposed scheme, CoRDS, the CSP is able to provide the services efficiently as per end-users requirements. In order to re-establish connectivity between the dumb nodes and the sink, we use a single leader multiple follower Stackelberg game. Additionally, theoretical characterization of CoRDS has been shown.
Integrative genomic and transcriptomic analysis for pinpointing recurrent alterations of plant homeodomain genes and their clinical significance in breast cancer

A wide range of the epigenetic effectors that regulate chromatin modification, gene expression, genomic stability, and DNA repair contain structurally conserved domains called plant homeodomain (PHD) fingers. Alternations of several PHD finger-containing proteins (PHFs) due to genomic amplification, mutations, deletions, and translocations have been linked directly to various types of cancer. However, little is known about the genomic landscape and the clinical significance of PHFs in breast cancer. Hence, we performed a large-scale genomic and transcriptomic analysis of 98 PHF genes in breast cancer using TCGA and METABRIC datasets and correlated the recurrent alterations with clinicopathological features and survival of patients. Different subtypes of breast cancer had different patterns of copy number and expression for each PHF. We identified a subset of PHF genes that was recurrently altered with high prevalence, including PYGO2 (pygopus family PHD finger 2), ZMYND8 (zinc finger, MYND-type containing 8), ASXL1 (additional sex combs like 1) and CHD3 (chromodomain helicase DNA binding protein 3). Copy number increase and overexpression of ZMYND8 were more prevalent in Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. ZMYND8 was also involved in a positive feedback circuit of the estrogen receptor (ER) pathway, and the expression of ZMYND8 was repressed by the bromodomain and extra terminal (BET) inhibitor in breast cancer. Our findings suggest a promising avenue for future research—to focus on a subset of PHFs to better understand the molecular mechanisms and to identify therapeutic targets in breast cancer.
Data-driven finite elements for geometry and material design

Crafting the behavior of a deformable object is difficult---whether it is a biomechanically accurate character model or a new multimaterial 3D printable design. Getting it right requires constant iteration, performed either manually or driven by an automated system. Unfortunately, Previous algorithms for accelerating three-dimensional finite element analysis of elastic objects suffer from expensive precomputation stages that rely on a priori knowledge of the object's geometry and material composition. In this paper we introduce Data-Driven Finite Elements as a solution to this problem. Given a material palette, our method constructs a metamaterial library which is reusable for subsequent simulations, regardless of object geometry and/or material composition. At runtime, we perform fast coarsening of a simulation mesh using a simple table lookup to select the appropriate metamaterial model for the coarsened elements. When the object's material distribution or geometry changes, we do not need to update the metamaterial library---we simply need to update the metamaterial assignments to the coarsened elements. An important advantage of our approach is that it is applicable to non-linear material models. This is important for designing objects that undergo finite deformation (such as those produced by multimaterial 3D printing). Our method yields speed gains of up to two orders of magnitude while maintaining good accuracy. We demonstrate the effectiveness of the method on both virtual and 3D printed examples in order to show its utility as a tool for deformable object design.
Fatigue and Muscle Strength Involving Walking Speed in Parkinson's Disease: Insights for Developing Rehabilitation Strategy for PD

Background. Problems with gait in Parkinson's disease (PD) are a challenge in neurorehabilitation, partly because the mechanisms causing the walking disability are unclear. Weakness and fatigue, which may significantly influence gait, are commonly reported by patients with PD. Hence, the aim of this study was to investigate the association between weakness and fatigue and walking ability in patients with PD. Methods. We recruited 25 patients with idiopathic PD and 25 age-matched healthy adults. The maximum voluntary contraction (MVC), twitch force, and voluntary activation levels were measured before and after a knee fatigue exercise. General fatigue, central fatigue, and peripheral fatigue were quantified by exercise-induced changes in MVC, twitch force, and activation level. In addition, subjective fatigue was measured using the Multidimensional Fatigue Inventory (MFI) and Fatigue Severity Scale (FSS). Results. The patients with PD had lower activation levels, more central fatigue, and more subjective fatigue than the healthy controls. There were no significant differences in twitch force or peripheral fatigue index between the two groups. The reduction in walking speed was related to the loss of peripheral strength and PD itself. Conclusion. Fatigue and weakness of central origin were related to PD, while peripheral strength was important for walking ability. The results suggest that rehabilitation programs for PD should focus on improving both central and peripheral components of force.
NS2: Networked Searchable Store with Correctness

In an outsourced data framework, we introduce and demonstrate mechanisms for securely storing a set of data items (documents) on an un-trusted server, while allowing for subsequent conjunctive keyword searches for matching documents. The protocols provide full computational privacy, query correctness assurances and no leaks: the server either correctly executes client queries or (if it behaves maliciously) is immediately detected. The client is then provided with strong assurances proving the authenticity and completeness of results. This is different from existing secure keyword search research efforts where a cooperating, non-malicious server behavior is assumed. Additionally, not only does the oblivious search protocol conceal the outsourced data (from the un-trusted server) but it also does not leak client access patterns, the queries themselves, the association between different queries or between newly added documents and their corresponding keywords (not even in encrypted form). These assurances come at the expense of additional computation costs which we analyze in the context of today's hardware.
MARCO, TLR2, and CD14 Are Required for Macrophage Cytokine Responses to Mycobacterial Trehalose Dimycolate and Mycobacterium tuberculosis

Virtually all of the elements of Mycobacterium tuberculosis (Mtb) pathogenesis, including pro-inflammatory cytokine production, granuloma formation, cachexia, and mortality, can be induced by its predominant cell wall glycolipid, trehalose 6,6′-dimycolate (TDM/cord factor). TDM mediates these potent inflammatory responses via interactions with macrophages both in vitro and in vivo in a myeloid differentiation factor 88 (MyD88)-dependent manner via phosphorylation of the mitogen activated protein kinases (MAPKs), implying involvement of toll-like receptors (TLRs). However, specific TLRs or binding receptors for TDM have yet to be identified. Herein, we demonstrate that the macrophage receptor with collagenous structure (MARCO), a class A scavenger receptor, is utilized preferentially to “tether” TDM to the macrophage and to activate the TLR2 signaling pathway. TDM-induced signaling, as measured by a nuclear factor-kappa B (NF-κB)-luciferase reporter assay, required MARCO in addition to TLR2 and CD14. MARCO was used preferentially over the highly homologous scavenger receptor class A (SRA), which required TLR2 and TLR4, as well as their respective accessory molecules, in order for a slight increase in NF-κB signaling to occur. Consistent with these observations, macrophages from MARCO−/− or MARCO−/−SRA−/− mice are defective in activation of extracellular signal-related kinase 1/2 (ERK1/2) and subsequent pro-inflammatory cytokine production in response to TDM. These results show that MARCO-expressing macrophages secrete pro-inflammatory cytokines in response to TDM by cooperation between MARCO and TLR2/CD14, whereas other macrophage subtypes (e.g. bone marrow–derived) may rely somewhat less effectively on SRA, TLR2/CD14, and TLR4/MD2. Macrophages from MARCO−/− mice also produce markedly lower levels of pro-inflammatory cytokines in response to infection with virulent Mtb. These observations identify the scavenger receptors as essential binding receptors for TDM, explain the differential response to TDM of various macrophage populations, which differ in their expression of the scavenger receptors, and identify MARCO as a novel component required for TLR signaling.
Syphilis: New Diagnostic Directions

The development of the Treponema pallidum haemagglutination assay (TPHA) in the mid-1960s1,2 led to its widespread use in Europe as a screening test, usually in combination with a cardiolipin antigen test3-5. This combination was acknowledged as giving the best coverage for detection or exc~usion of all forms of treponemal infection", and m t.he United Kingdom in 1983, 86% of laborat? nes participating in the United Kingdom (UK) National External Quality Assessment Scheme for Microbiology employed this screening protocol>. In contrast to the stability in test protocols there was a marked change in the epidemiology of early syphilis with a significant overall decline in incidence in the United Kingdom starting in the late 1970s (Figure 1). As a result of this decrease the value of traditional routine testing of certain populations such as pregnant women" and blood donors7 has been questioned. Over the past few years the situation has changed and we have witnessed important potential developments in the diagnosis of syphilis's? as well as a renewed interest in many aspects of the disease itself 14. Factors associated with this renaissance include: interactions between syphilis and infection with the human immunodeficiency virus (HIV)15-21; changes in the epidemiology of early syphilis22-25 production of pathogen-specific monoclonal
Pro- and anti-inflammatory roles of interleukin-1 in recurrence of bacterial cell wall-induced arthritis in rats

A specific interleukin-1 (IL-1) receptor antagonist (IL-1ra) was used to examine the roles of IL-1 in an experimental model designed to analyze the reactivation phase of erosive arthritis, induced in rats with peptidoglycan-polysaccharide polymers (PG-APS) isolated from cell walls of group A streptococci. Monoarticular arthritis was initiated by injection of a small dose of PG-APS into an ankle joint, and reactivation was induced by intravenous injection of PG-APS 20 days later. Human recombinant IL-1ra given at a dose of 2 to 3 mg/kg at the time of reactivation of arthritis and at 6-h intervals inhibits the increase in joint swelling by at least 60%. Joint swelling is suppressed 30 to 50% when the initial treatment with IL-1ra is delayed until 6 h after reactivation. IL-1ra is not effective when the initial injection is delayed 12 or 24 h. With an injection schedule of IL-1ra given at the time of reactivation and every 6 h, treatment can be stopped at 24 h and the suppression of swelling is no different from that in rats for which injections are continued for 4 days. The results indicate that IL-1 has a prominent, although not exclusive, role in initiating inflammation in this model and is involved in the amplifying processes in progressive inflammation and chronic erosive disease. An anti-inflammatory function of IL-1 is also indicated from data showing that IL-1ra treatment limited to 6 h or less after the induction of reactivation enhances joint swelling, whereas intravenous injection of human recombinant IL-1 beta 24 h before reactivation suppresses the reactivation of arthritis.
Beyond a warming fingerprint: individualistic biogeographic responses to heterogeneous climate change in California

Understanding recent biogeographic responses to climate change is fundamental for improving our predictions of likely future responses and guiding conservation planning at both local and global scales. Studies of observed biogeographic responses to 20th century climate change have principally examined effects related to ubiquitous increases in temperature – collectively termed a warming fingerprint. Although the importance of changes in other aspects of climate – particularly precipitation and water availability – is widely acknowledged from a theoretical standpoint and supported by paleontological evidence, we lack a practical understanding of how these changes interact with temperature to drive biogeographic responses. Further complicating matters, differences in life history and ecological attributes may lead species to respond differently to the same changes in climate. Here, we examine whether recent biogeographic patterns across California are consistent with a warming fingerprint. We describe how various components of climate have changed regionally in California during the 20th century and review empirical evidence of biogeographic responses to these changes, particularly elevational range shifts. Many responses to climate change do not appear to be consistent with a warming fingerprint, with downslope shifts in elevation being as common as upslope shifts across a number of taxa and many demographic and community responses being inconsistent with upslope shifts. We identify a number of potential direct and indirect mechanisms for these responses, including the influence of aspects of climate change other than temperature (e.g., the shifting seasonal balance of energy and water availability), differences in each taxon's sensitivity to climate change, trophic interactions, and land‐use change. Finally, we highlight the need to move beyond a warming fingerprint in studies of biogeographic responses by considering a more multifaceted view of climate, emphasizing local‐scale effects, and including a priori knowledge of relevant natural history for the taxa and regions under study.
Free triiodothyronine has a distinct circadian rhythm that is delayed but parallels thyrotropin levels.

CONTEXT TSH is known to have a circadian rhythm, but the relationship between this and any rhythm in T(4) and T(3) has not been clearly demonstrated. OBJECTIVE With a view to optimizing thyroid hormone replacement therapy, we have used modern assays for free T(4) (FT4) and free T(3) (FT3) to investigate circadian rhythmicity. SETTING The study was performed at a university hospital. DESIGN AND SUBJECTS This was a cross-sectional study in 33 healthy individuals with 24-h blood sampling (TSH in 33 and FT4 and FT3 in 29 individuals) and cosinor analysis. RESULTS Of the individuals, 100% showed a sinusoidal signal in TSH, for FT4 76%, and for FT3 86% (P < 0.05). For FT4 and FT3, the amplitude was low. For TSH the acrophase occurred at a clock time of 0240 h, and for FT3 approximately 90 minutes later at 0404 h. The group cosinor model predicts that TSH hormone levels remain above the mesor between 2020 and 0820 h, and for FT3 from 2200-1000 h. Cross correlation of FT3 with TSH showed that the peak correlation occurred with a delay of 0.5-2.5 h. When time-adjusted profiles of TSH and FT3 were compared, there was a strong correlation between FT3 and TSH levels (rho = 0.80; P < 0.0001). In contrast, cross correlation revealed no temporal relationship between FT4 and TSH. CONCLUSIONS FT3 shows a circadian rhythm with a periodicity that lags behind TSH, suggesting that the periodic rhythm of FT3 is due to the proportion of T(3) derived from the thyroid. Optimizing thyroid hormone replacement may need to take these rhythms into account.
Effects of transplantation on the primitive immunohematopoietic stem cell

Transplantation has strong deleterious effects on the primitive immunohematopoietic stem cells (PSC) from which circulating lymphocytes and erythrocytes are descended. We studied these effects over 300-400 d, testing whether PSC numbers, repopulating abilities, or both, were reduced. Equivalent PSC numbers were estimated in recipients of mixtures of genetically different cells, using the binomial model with covariance. Percentages of lymphocyte and erythrocyte types were closely correlated, as were percentages of either type sampled at intervals of several months. This suggests that the same PSC produced lymphoid and myeloid cells, and that most circulating cells were descended from the same PSC over hundreds of days. Equivalent PSC concentrations were approximately 1/10(5) fresh marrow cells, and were about twofold lower using previously transplanted marrow. However, such marrow repopulated only one-seventh to one-eighth as well as fresh marrow. Apparently, transplantation not only reduces PSC concentrations, but also reduces the repopulating ability per PSC. This may result from excessive stimuli to differentiate that overbalance the stimuli for PSC to replenish themselves.
Microcontact printing of P‐selectin increases the rate of neutrophil recruitment under shear flow

The local variation of P‐selectin expression on inflamed endothelial layers affects leukocyte recruitment in vivo. As an initial study of the spatially heterogeneous presentation of P‐selectin in vitro, the influence of microcontact printing (μCP) of P‐selectin on a planar surface in neutrophil recruitment was investigated using a parallel‐plate flow chamber. Microline patterned and nonpatterned P‐selectin were prepared using PDMS, Poly(dimethylsiloxane) (PMDS) stamps and isolated neutrophils perfused over the surface to quantify the level of neutrophil recruitment. We first found a significant increase in cell rolling flux and a decrease in cell rolling velocity on the microcontact printed P‐selectin‐surfaces compared with a randomly adsorbed P‐selectin‐surface. However, the increase in rolling adhesion under shear on the surfaces prepared by μCP was not proportional to the number of functional sites of P‐selectin transferred using immunofluorescent labeling. Interestingly, the relative immunofluorescent intensities of the nonfunctional regions of microcontact printed P‐selectin‐surfaces were substantially lower than that that of randomly adsorbed P‐selectin. Taken together, these data indicate that the μCP of selectin increases the transfer rate of the adhesion molecule on a surface in the functionally correct orientation and, consequently, improves the recruitment of leukocytes to the selectin surface under flow. It is concluded that μCP may be a more general technique to control protein orientation on a substrate.
Electrical Signals of Memory and of the Awareness of Remembering

Learning factual information and accurately remembering specific experiences from the past are central to human intellectual and social life. These extraordinary abilities require computations on diverse sorts of information represented in the brain. Networks of neurons in the cerebral cortex are specialized for analyzing and representing such information, whereas the storage of facts and events within these networks depends fundamentally on linking multiple representational fragments together. This cross-cortical linking function is disrupted in patients with amnesia. Electrical measures of the brain in action, obtained while people perform feats of memory in laboratory settings, have been used to investigate the storage and retrieval of facts and episodes. Electrical signals associated with specific aspects of memory processing have been identified through research that constitutes part of a larger scientific endeavor aimed at understanding memory, the subjective experience of remembering that can accompany retrieval, and disorders of memory that can result from brain damage.
Targeted surveillance to assess the presence of BSE in the age risk population of cattle slaughtered in Bursa, Turkey: preliminary results of an immunohistochemical detection study for the 2004-2005 period

Bovine spongiform encephalopathy (BSE), a member of the transmissible spongiform encepahlopathies, has been a notifiable disease in Turkey since 1997. In 2002, the BSE status of Turkey was assessed by the EU Scientific Steering Committee as "it is likely but not confirmed". This study presents the results of a targeted surveillance study to assess the presence of BSE in the age risk population of Bursa, Turkey. In the assessment procedure, the immunohistochemical detection of protease-resistant prion protein (PrP-Sc) was aimed at and applied to 420 brain tissues of cattle slaughtered in Bursa at an age of 30-months and older. None of the samples were positive for BSE.
Comparison of the compression characteristics of 2D braided and circular knitted carbon/epoxy composite tubes

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PM - protein music

We present the program PM for the analysis of protein sequence information using audification. Audification is the technique of using the sense of hearing to analyse data (Jackson, 1993). The advantage of audification over visualisation in data analysis is that sound has the property that when different notes are played together they can still be individually heard: in vision colours blend to form new colours. This distinction can be very useful when studying multivariate data. The one dimensional structure of DNA maps naturally onto musical sequences (Hayashi and Munakata, 1984; Ohno and Ohno, 1986). The mapping algorithm in PM is designed to translate coding sequences into sound in a way that is more harmonious and more open to analysis than previous methods. The PM algorithm uses the DNA nucleotide sequence to form the musical top line, and the properties of the translated amino-acids to form the bass line. The notes are in the scale of C Major and there are three beats to the bar. Each codon corresponds to a bar of music and the notes are played on the beat in order of nucleotide sequence. The mapping of the top line to musical notes is as follows: A4 submediant E3 mediant C3 tonic G3 dominant The mapping of the bass line to notes is more complicated and is based on the designation of aminoacid physico-chemical properties of Taylor (1983). Each of the properties has a note assigned to it. The mapping is as follows: polar hydrophobic charged positive aliphatic aromatic tiny