Miracle-dz/UniFAR-FTUs huggingface dataset:
N-glycolyl groups of nonhuman chondroitin sulfates survive in ancient fossils

Significance We identified a glycan modification called N-glycolylated chondroitin sulfate (Gc-CS), derived from metabolic turnover of the nonhuman sialic acid N-glycolylneuraminic acid (Neu5Gc). The presence of Gc-CS could be demonstrated in species rich in Neu5Gc using chemically synthesized Gc-CS as a standard for mass spectrometry. Although humans cannot synthesize Neu5Gc due to a loss-of-function mutation, trace amounts of Gc-CS were found in humans, apparently derived from Neu5Gc-containing foods. Gc-CS was more easily detectable in animal fossils as old as 4 My, allowing indirect fossil evidence of Neu5Gc expression. These findings enable future studies to date the loss of Neu5Gc biosynthesis during human evolution and investigate this glycosaminoglycan modification in humans who consume Neu5Gc-rich foods (red meats). Biosynthesis of the common mammalian sialic acid N-glycolylneuraminic acid (Neu5Gc) was lost during human evolution due to inactivation of the CMAH gene, possibly expediting divergence of the Homo lineage, due to a partial fertility barrier. Neu5Gc catabolism generates N-glycolylhexosamines, which are potential precursors for glycoconjugate biosynthesis. We carried out metabolic labeling experiments and studies of mice with human-like Neu5Gc deficiency to show that Neu5Gc degradation is the metabolic source of UDP-GlcNGc and UDP-GalNGc and the latter allows an unexpectedly selective incorporation of N-glycolyl groups into chondroitin sulfate (CS) over other potential glycoconjugate products. Partially N-glycolylated-CS was chemically synthesized as a standard for mass spectrometry to confirm its natural occurrence. Much lower amounts of GalNGc in human CS can apparently be derived from Neu5Gc-containing foods, a finding confirmed by feeding Neu5Gc-rich chow to human-like Neu5Gc-deficient mice. Unlike the case with Neu5Gc, N-glycolyl-CS was also stable enough to be detectable in animal fossils as old as 4 My. This work opens the door for investigating the biological and immunological significance of this glycosaminoglycan modification and for an “ancient glycans” approach to dating of Neu5Gc loss during the evolution of Homo.
iFER: facial expression recognition using automatically selected geometric eye and eyebrow features

Abstract. Facial expressions have an important role in interpersonal communications and estimation of emotional states or intentions. Automatic recognition of facial expressions has led to many practical applications and became one of the important topics in computer vision. We present a facial expression recognition system that relies on geometry-based features extracted from eye and eyebrow regions of the face. The proposed system detects keypoints on frontal face images and forms a feature set using geometric relationships among groups of detected keypoints. Obtained feature set is refined and reduced using the sequential forward selection (SFS) algorithm and fed to a support vector machine classifier to recognize five facial expression classes. The proposed system, iFER (eye–eyebrow only facial expression recognition), is robust to lower face occlusions that may be caused by beards, mustaches, scarves, etc. and lower face motion during speech production. Preliminary experiments on benchmark datasets produced promising results outperforming previous facial expression recognition studies using partial face features, and comparable results to studies using whole face information, only slightly lower by ∼ 2.5 % compared to the best whole face facial recognition system while using only ∼ 1 / 3 of the facial region.
Motor execution detection based on autonomic nervous system responses

Triggered assistance has been shown to be a successful robotic strategy for provoking motor plasticity, probably because it requires neurologic patients’ active participation to initiate a movement involving their impaired limb. Triggered assistance, however, requires sufficient residual motor control to activate the trigger and, thus, is not applicable to individuals with severe neurologic injuries. In these situations, brain and body–computer interfaces have emerged as promising solutions to control robotic devices. In this paper, we investigate the feasibility of a body–machine interface to detect motion execution only monitoring the autonomic nervous system (ANS) response. Four physiological signals were measured (blood pressure, breathing rate, skin conductance response and heart rate) during an isometric pinching task and used to train a classifier based on hidden Markov models. We performed an experiment with six healthy subjects to test the effectiveness of the classifier to detect rest and active pinching periods. The results showed that the movement execution can be accurately classified based only on peripheral autonomic signals, with an accuracy level of 84.5%, sensitivity of 83.8% and specificity of 85.2%. These results are encouraging to perform further research on the use of the ANS response in body–machine interfaces.
Deep evaluation of hybrid architectures: use of different metrics in MERT weight optimization

The process of developing hybrid MT systems is usually guided by an evaluation method used to compare different combinations of basic subsystems. This work presents a deep evaluation experiment of a hybrid architecture, which combines rule-based and statistical translation approaches. Differences between the results obtained from automatic and human evaluations corroborate the inappropriateness of pure lexical automatic evaluation metrics to compare the outputs of systems that use very different translation approaches. An examination of sentences with controversial results suggested that linguistic well-formedness should be considered in the evaluation of output translations. Following this idea, we have experimented with a new simple automatic evaluation metric, which combines lexical and PoS information. This measure showed higher agreement with human assessments than BLEU in a previous study (Labaka et al., 2011). In this paper we have extended its usage throughout the system development cycle, focusing on its ability to improve parameter optimization. Results are not totally conclusive. Manual evaluation reflects a slight improvement, compared to BLEU, when using the proposed measure in system optimization. However, the improvement is too small to draw any clear conclusion. We believe that we should first focus on integrating more linguistically representative features in the developing of the hybrid system, and then go deeper into the development of automatic evaluation metrics.
The Use of Humor in Palliative Care: A Systematic Literature Review

Background: Humor has its own place in the context of medicine. Nevertheless, its acceptance by terminal stage patients and health-care professionals has not been studied in depth and is not free from controversy. Objectives: To understand the significance, appropriateness, and pertinence of the use of humor in palliative care and to analyze its applicability. Design: A narrative systematic review was undertaken and included in PROSPERO. Data Sources: Online searches were carried out on PUBMED, PSYCINFO, EBSCO (CINHAL), EMBASE, SCIELO, SCOPUS, TESEO, WEB of SCIENCE, and COCHRANE between their launch date and December 31, 2015, complemented with manual searches with queries to experts. A total of 156 studies were identified, which were then filtered in pairs by means of an established hierarchy, selecting studies that discussed the use of humor specifically in palliative care from all perspectives and designs, and finally published in Spanish, English, French, or Portuguese. Critical reading of all the selected studies took place, with no exclusions due to quality evaluation. Results: Thirty-four studies were included. Five main topics were identified: (1) definition of humor, (2) use and functions of humor in palliative care, (3) how to use humor, (4) when not to use humor, and (5) humor before and after the diagnosis of terminal illness. Conclusions: Humor plays an unquestionable role in palliative care, but its use needs training and appropriate use.
Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH

Live imaging of genome has offered important insights into the dynamics of the genome organization and gene expression. The demand to image simultaneously multiple genomic loci has prompted a flurry of exciting advances in multi-color CRISPR imaging, although color-based multiplexing is limited by the need for spectrally distinct fluorophores. Here we introduce an approach to achieve highly multiplexed live recording via correlative CRISPR imaging and sequential DNA fluorescence in situ hybridization (FISH). This approach first performs one-color live imaging of multiple genomic loci and then uses sequential rounds of DNA FISH to determine the loci identity. We have optimized the FISH protocol so that each round is complete in 1 min, demonstrating the identification of 7 genomic elements and the capability to sustain reversible staining and washing for up to 20 rounds. We have also developed a correlation-based algorithm to faithfully register live and FISH images. Our approach keeps the rest of the color palette open to image other cellular phenomena of interest, as demonstrated by our simultaneous live imaging of genomic loci together with a cell cycle reporter. Furthermore, the algorithm to register faithfully between live and fixed imaging is directly transferrable to other systems such as multiplex RNA imaging with RNA-FISH and multiplex protein imaging with antibody-staining.
Na+-K+-ATPase and Na+/Ca2+ exchange activities in gills of hyperregulating Carcinus maenas.

Na+-K+-ATPase and Na+/Ca2+exchange activities were studied in gills of Carcinus maenas in seawater (SW) and after transfer to dilute seawater (DSW). Carcinushyperregulates its hemolymph osmolarity through active uptake of Na+, Cl-, and Ca2+. In DSW total Na+-K+-ATPase activity in posterior gills quadrupled; Na+/Ca2+ exchange specific activity was unaffected, and total activity increased 1.67-fold. Short-circuit current ( I sc) in voltage-clamped posterior gill hemilamellae was -181 μA/cm2 in SW and -290 μA/cm2 in DSW and up to 90% ouabain sensitive; conductivity was similar in SW or DSW (42 and 46 mS/cm2, respectively) and representative of a leaky epithelium. The new steady state of hemolymph osmolarity 24 h after DSW transfer was preceded, already 3 h after transfer, by increased Na+-K+-ATPase but not Na+/Ca2+exchange activity. Western blot analysis indicated that the amount of Na+-K+-ATPase protein had increased 2.1-fold in crabs acclimated 3 wk to DSW; however, 4 h after DSW transfer no difference in the amount of Na+-K+-ATPase protein was observed. After DSW transfer branchial cAMP content decreased. A negative correlation between branchial Na+-K+-ATPase activity and cAMP content points to rapid regulation of Na+-K+-ATPase through cAMP-dependent protein kinase A activity. Ca2+ transport may depend on the high-capacity Na+/Ca2+exchanger coupled to the versatile sodium pump.
cAMP-dependent absorption of chloride across airway epithelium.

Elevated levels of Na and Cl in airway surface liquid may play a major role in the airway pathology of cystic fibrosis (CF) (J. J. Smith, S. M. Travis, E. P. Greenberg, and M. J. Welsh. Cell85: 229-236, 1996) and could be caused by block of transcellular Cl absorption due to lack of a functional CF transmembrane conductance regulator (CFTR). To test for transcellular absorption of Cl across non-CF epithelium, we studied how fluid absorption was affected by the opening and closing of Cl channels. Forskolin (an activator of CFTR) tripled fluid absorption across primary cultures of bovine tracheal epithelium but had no effect on human cells. However, in both species, fluid absorption was markedly inhibited by 5-nitro-2-(3-phenylpropylamino)benzoate, a blocker of CFTR. Microelectrode studies suggested that the magnitude of the absorptive response to forskolin in bovine cells depended on the size of an inwardly directed electrochemical driving force for Cl movement across the apical membrane. Patch-clamp measurements of bovine cells revealed CFTR in the apical membrane and a cAMP-activated, inwardly rectifying Cl channel in the basolateral membrane. We conclude that a significant fraction of absorbed Cl passes transcellularly in bovine tracheal epithelial cultures, with CFTR as the path of entry in the apical membrane and a novel cAMP-activated Cl channel as the exit route in the basolateral membrane. Our data further indicate that a similar pathway may exist in non-CF human tracheal epithelium.
Decompression sickness risk in rats by microbial removal of dissolved gas.

We present a method for reducing the risk of decompression sickness (DCS) in rats exposed to high pressures of H2. Suspensions of the human colonic microbe Methanobrevibacter smithii were introduced via a colonic cannula into the large intestines of the rats. While the rats breathed H2 in a hyperbaric chamber, the microbe metabolized some of the H2diffusing into the intestine, converting H2 and CO2 to methane and water. Rate of release of methane from the rats, which was monitored by gas chromatography, varied with chamber H2 pressure. This rate was higher during decompression than during compression, suggesting that during decompression the microbe was metabolizing H2 stored in the rats' tissues. Rats treated with M. smithii had a 25% (5 of 20) incidence of DCS, which was significantly lower ( P < 0.01) than the 56% (28 of 50) incidence of untreated controls, brought on by a standardized compression and decompression sequence. Thus using a microbe in the intestine to remove an estimated 5% of the body burden of H2 reduced DCS risk by more than one-half. This method of biochemical decompression may potentially facilitate human diving.
Robust Adaptive Beamforming With a Novel Interference-Plus-Noise Covariance Matrix Reconstruction Method

Recently, a new robust adaptive beamforming (RAB) technique was proposed to remove the signal of interest (SOI) component from the sample covariance matrix based on interference-plus-noise covariance matrix reconstruction, which utilizes the Capon spectrum estimator integrated over a region separated from the direction of the SOI. However, the extreme condition of the reconstruction-based technique, that the precise information about the array structure is known in advance, is almost impossible in practice. In this paper, a novel method to reconstruct the interference-plus-noise covariance matrix is proposed. Considering the imprecise prior information about the array structure, which means that the array may be uncalibrated, we use an annulus uncertainty set to constrain the steering vectors of the interferences. Then we integrate the Capon spectrum over the surface of the annulus, by which we can obtain the reconstructed interference matrix without containing the SOI. Since the integral interval is a high-dimensional domain, which is very difficult to solve, we use a discrete sum method to calculate the integral approximately. With the reconstructed interference-plus-noise matrix, the nominal steering vector can be corrected via maximizing the beamformer output power by solving a quadratically constrained quadratic programming (QCQP) problem. The previous reconstruction method can be seen as a special case of the proposed one. The main advantage is that the proposed algorithm is robust against unknown arbitrary-type mismatches. Theoretical analysis and simulation results demonstrate the effectiveness and robustness of the proposed algorithm.
Theoretical and experimental studies on manipulation of fluorescence by gold nanoparticle: Application for molecular imaging

THEORETICAL AND EXPERIMENTAL STUDIES ON MANIPULATION OF FLUORESCENCE BY GOLD NANOPARTICLE: APPLICA TION FOR MOLECULAR IMAGING Jianting Wang December 2011 Gold nanopartic1es (GNPs) have shown beneficial properties for biomedical use, e.g., their non-toxic nature and surface properties for easy modification. Upon receiving light, they generate a strong surface plasmon field, which can alter the fluorescence of fluorophores. The level and type of the fluorescence alteration depend on the GNP size and shape, excitation (Ex)/emission (Em) wavelengths and quantum yield of the fluorophore, as well as the distance between the fluorophore and GNP. In this dissertation, the effect of the properties listed above on the fluorescence output was theoretically analyzed for the fluorophores frequently used in biomedical studies. For fluorescence quenching, fluorophores with the Em wavelength near the GNP plasmon resonance peak (520 nm) are better suited. As the Em wavelength increases, a shorter distance is required for achieving the same level of quenching. A bigger GNP requires shorter distance for quenching. To obtain fluorescence enhancement, the Em wavelength of the fluorophore needs to be longer than the GNP plasmon resonance peak (e.g., > 650 nm). The fluorophore with lower intrinsic quantum yield tends to be
Mental Algorithms in the Historical Emergence of Word Meanings

Words frequently acquire new senses, but the mental process that underlies the historical emergence of these senses is often opaque. Many have suggested that word meanings develop in non-arbitrary ways, but no attempt has been made to formalize these proposals and test them against historical data at scale. We propose that word meaning extension should reflect a drive towards cognitive economy. We test this proposal by exploring a family of computational models that predict the evolution of word senses, evaluated against a large digitized lexicon that dates back 1000 years in English language history. Our findings suggest that word meanings not only extend in predictable ways, but also that they do so following an historical path that tends to minimize cognitive cost through a process of nearestneighbor chaining. Our work contributes a formal approach to reverse-engineering mental algorithms of the human lexicon.
A Simple and E±cient Arrowhead Detection Technique in Biomedical Images

In biomedical documents/publications, medical images tend to be complex by nature and often contain severalregions that are annotated using arrows. In this context, an automated arrowhead detectionisa criticalprecursortoregion-of-interest(ROI)labelingandimagecontent analysis.To detect arrowheads, in this paper, images are ¯rst binarized using fuzzy binarization technique to segment a set of candidates based on connected component (CC) principle. To select arrow candidates, we use convexity defect-based ¯ltering, which is followed by template matching via dynamic time warping (DTW). The DTW similarity score con¯rms the presence of arrows in the image. Our test results on biomedical images from imageCLEF 2010 collection shows the interest of the technique, and can be compared with previously reported state-of-the-art results. *
Deletional Self-Tolerance to a Melanocyte/Melanoma Antigen Derived from Tyrosinase Is Mediated by a Radio-Resistant Cell in Peripheral and Mesenteric Lymph Nodes1

Self-tolerance to melanocyte differentiation Ags limits the ability to generate therapeutic antimelanoma responses. However, the mechanisms responsible for CD8 T cell tolerance to these Ags are unknown. We have used a newly generated TCR-transgenic mouse to establish the basis of tolerance to one such Ag from tyrosinase. Despite expression of tyrosinase transcripts in the thymus, central deletion does not shape the tyrosinase-specific CD8 T cell repertoire. We demonstrate that this endogenously expressed melanocyte Ag is constitutively presented in both peripheral and mesenteric lymph nodes, leading to abortive activation and deletion of tyrosinase-specific CD8 T cells. Importantly, this Ag is not presented by either radio-sensitive dendritic cells, or by radio-resistant Langerhans cells. Thus, for this endogenous Ag, cross-tolerization does not appear to be an operative mechanism. Instead, we find radioresistant tyrosinase mRNA expression in lymphoid compartments where CD8 T cell deletion occurs. This suggests that direct presentation of tyrosinase by radio-resistant lymph node resident cells is entirely responsible for tolerance to this endogenous melanocyte differentiation Ag.
Prostate cancer screening—when to start and how to screen?

Prostate-specific antigen (PSA) screening reduces prostate cancer (PCa) mortality; however such screening may lead to harm in terms of overdiagnosis and overtreatment. Therefore, upfront shared decision making involving a discussion about pros and cons between a physician and a patient is crucial. Total PSA remains the most commonly used screening tool and is a strong predictor of future life-threatening PCa. Currently there is no strong consensus on the age at which to start PSA screening. Most guidelines recommend PSA screening to start no later than at age 55 and involve well-informed men in good health and a life expectancy of at least 10–15 years. Some suggest to start screening in early midlife for men with familial predisposition and men of African-American descent. Others suggest starting conversations at age 45 for all men. Re-screening intervals can be risk-stratified as guided by the man’s age, general health and PSA-value; longer intervals for those at lower risk and shorter intervals for those at higher risk. Overdiagnosis and unnecessary biopsies can be reduced using reflex tests. Magnetic resonance imaging in the pre-diagnostic setting holds promise in pilot studies and large-scale prospective studies are ongoing.
Investigating the hybrid textures of neutrino mass matrix for near maximal atmospheric neutrino mixing

In the present paper, we have studied that the implication of a large value of the effective Majorana neutrino mass in case of neutrino mass matrices having either two equal elements and one zero element (popularly known as hybrid texture) or two equal cofactors and one zero minor (popularly known as inverse hybrid texture) in the flavor basis. In each of these cases, four out of sixty phenomenologically possible patterns predict near maximal atmospheric neutrino mixing angle in the limit of large effective Majorana neutrino mass. This feature remains irrespective of the experimental data on solar and reactor mixing angles. In addition, we have also performed the comparative study of all the viable cases of hybrid and inverse hybrid textures at 3$\sigma$ CL.
BiggerPicture

Filling a small hole in an image with plausible content is well studied. Extrapolating an image to give a distinctly larger one is much more challenging---a significant amount of additional content is needed which matches the original image, especially near its boundaries. We propose a data-driven approach to this problem. Given a source image, and the amount and direction(s) in which it is to be extrapolated, our system determines visually consistent content for the extrapolated regions using library images. As well as considering low-level matching, we achieve consistency at a higher level by using graph proxies for regions of source and library images. Treating images as graphs allows us to find candidates for image extrapolation in a feasible time. Consistency of subgraphs in source and library images is used to find good candidates for the additional content; these are then further filtered. Region boundary curves are aligned to ensure consistency where image parts are joined using a photomontage method. We demonstrate the power of our method in image editing applications.