Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mycobacterium tuberculosis complex has a pathway for the biosynthesis of 4‐formamido‐4,6‐dideoxy‐d‐glucose

Recent studies have demonstrated that the O‐antigens of some pathogenic bacteria such as Brucella abortus, Francisella tularensis, and Campylobacter jejuni contain quite unusual N‐formylated sugars (3‐formamido‐3,6‐dideoxy‐d‐glucose or 4‐formamido‐4,6‐dideoxy‐d‐glucose). Typically, four enzymes are required for the formation of such sugars: a thymidylyltransferase, a 4,6‐dehydratase, a pyridoxal 5'‐phosphate or PLP‐dependent aminotransferase, and an N‐formyltransferase. To date, there have been no published reports of N‐formylated sugars associated with Mycobacterium tuberculosis. A recent investigation from our laboratories, however, has demonstrated that one gene product from M. tuberculosis, Rv3404c, functions as a sugar N‐formyltransferase. Given that M. tuberculosis produces l‐rhamnose, both a thymidylyltransferase (Rv0334) and a 4,6‐dehydratase (Rv3464) required for its formation have been identified. Thus, there is one remaining enzyme needed for the production of an N‐formylated sugar in M. tuberculosis, namely a PLP‐dependent aminotransferase. Here we demonstrate that the M. tuberculosis rv3402c gene encodes such an enzyme. Our data prove that M. tuberculosis contains all of the enzymatic activities required for the formation of dTDP‐4‐formamido‐4,6‐dideoxy‐d‐glucose. Indeed, the rv3402c gene product likely contributes to virulence or persistence during infection, though its temporal expression and location remain to be determined.
Electrochemical Enzyme Biosensors Revisited: Old Solutions for New Problems

ABSTRACT Worldwide legislation is driving the development of novel and highly efficient analytical tools for assessing the composition of every material that interacts with Consumers or Nature. The biosensor technology is one of the most active R&D domains of Analytical Sciences focused on the challenge of taking analytical chemistry to the field. Electrochemical biosensors based on redox enzymes, in particular, are highly appealing due to their usual quick response, high selectivity and sensitivity, low cost and portable dimensions. This review paper aims to provide an overview of the most important advances made in the field since the proposal of the first biosensor, the well-known hand-held glucose meter. The first section addresses the current needs and challenges for novel analytical tools, followed by a brief description of the different components and configurations of biosensing devices, and the fundamentals of enzyme kinetics and amperometry. The following sections emphasize on enzyme-based amperometric biosensors and the different stages of their development.
Purinergic P2Y Receptors Are Involved in Xenopus Head Formation

P2Y receptors belong to the family of G protein-coupled receptors and are activated by nucleotides in the extracellular space. We showed that Xenopus P2Y1 and P2Y11 were expressed in the dorsal marginal zone from early gastrula stage and enriched in the central nervous system from neurula stages. They were expressed in the prospective head region during early development. Knockdown of P2Y1 and P2Y11 caused head malformation, such as small eyes, brain atrophy, and defect in cartilage tissues, as well as reduced expression of neural, placode, and neural crest markers. Furthermore, the expression of neural plate and epidermal markers was affected by P2Y1 or P2Y11 depletion at early neurula stage, suggesting that P2Y1 or P2Y11 might be required for the neural induction. Our findings suggested that P2Y receptors might be involved in distinguishing between neural and non-neural fates. The results also suggested that P2Y1 or P2Y11 could play a role in neural induction and/or maintenance of neural tissues in the head formation processes.
Empirical study of the evaluation of perspectives to knowledge capitalisation in Brazilian software industry

Knowledge capitalisation directs the activities of use, exploitation and reuse of knowledge for performing new tasks, including technical and management aspects. Specifically, considering software development, knowledge capitalisation demands an analysis that considers four complementary and interdependent perspectives on knowledge: value, security, utility and status. These perspectives focus on different facets according to which knowledge can be analysed, in addition to provide a foundation for a better awareness on knowledge and the necessary treatment. This study presents an empirical study with the purpose of evaluating the relevance of these perspectives by using a survey questionnaire distributed to software development companies in the Brazilian market. Three hundred thirty nine individuals from different 339 companies were subjects of such a study. The results indicate that the perspectives are relevant for evaluating knowledge and reinforcing the relevance of exploring knowledge capitalisation in software development; therefore, there is a clear understanding of how the knowledge assets involved can be analysed or assessed.
Increasing the minimum Euclidean distance of the complex quadrature spatial modulation

Complex quadrature spatial modulation transmits two signal symbols at each channel use, each is drawn from a different constellation set. The indices of the antennas from which the symbols are transmitted carry information to the receiver. When both symbols are transmitted from the same antenna, the symbols resulting from the addition of the two signal symbols belong to the Minkowski sum of the original two constellation sets. Therefore, the size of the modulation set at the transmitter increases and the minimum distance between transmitted symbols is reduced, leading to degradation in the error performance. In this study, the authors propose to equip the transmitter with an additional antenna which is used to transmit the second signal symbol only when the information bits representing the antenna indices are identical. The design of the optimum modulation sets that maximise the Euclidean distance is also addressed. Furthermore, based on the probability of antenna use, they advise an antenna ranking algorithm that improves the performance. The simulation results show that the proposed scheme achieves a signal-to-noise ratio gain of 6.4 and 9.5 dB using 16 quadrature amplitude modulation and 16 phase-shift keying, respectively.
Incidence and prevalence of sporadic and hereditary MTC in Denmark 1960–2014: a nationwide study

Recent studies have shown a significant increase in the temporal trend of medullary thyroid carcinoma (MTC) incidence. However, it remains unknown to which extent sporadic medullary thyroid carcinoma (SMTC) and hereditary MTC (HMTC) affect the MTC incidence over time. We conducted a nationwide retrospective study using previously described RET and MTC cohorts combined with review of medical records, pedigree comparison and relevant nationwide registries. The study included 474 MTC patients diagnosed in Denmark between 1960 and 2014. In the nationwide period from 1997 to 2014, we recorded a mean age-standardized incidence of all MTC, SMTC and HMTC of 0.19, 0.13 and 0.06 per 100,000 per year, respectively. The average annual percentage change in incidence for all MTC, SMTC and HMTC were 1.0 (P = 0.542), 2.8 (P = 0.125) and −3.1 (P = 0.324), respectively. The corresponding figures for point prevalence at January 1, 2015 were 3.8, 2.5 and 1.3 per 100,000, respectively. The average annual percentage change in prevalence from 1998 to 2015 for all MTC, SMTC and HMTC was 2.8 (P < 0.001), 3.8 (P < 0.001) and 1.5 (P = 0.010), respectively. We found no significant change in the incidence of all MTC, SMTC and HMTC possibly due to our small sample size. However, due to an increasing trend in the incidence of all MTC and opposing trends of SMTC (increasing) and HMTC (decreasing) incidence, it seems plausible that an increase for all MTC seen by others may be driven by the SMTC group rather than the HMTC group.
Whole exome sequencing identifies PLEC, EXO5 and DNAH7 as novel susceptibility genes in testicular cancer

Testicular germ cell tumors (TGCTs) are a clinically and pathologically heterogeneous disease, and little is known of its genetic basis. Only low susceptibility risk loci have been identified for both sporadic and familial cases. Therefore, we tried to identify new susceptibility genes responsible for familial testicular cancer that may contribute to increasing our knowledge about the genetic basis of the disease. Nineteen Spanish families with at least two affected individuals with TGCT were selected. WES was performed on those individuals using an Illumina Hiseq2000 sequencing platform. Data were analyzed under a monogenic and polygenic model of inheritance, and candidate variants were evaluated in a case–control association study performed on 391 Spanish sporadic cases and 1,170 healthy Spanish controls. Results were replicated in a second series consisting of 101 TGCTs from the Cancer Genome Atlas (TGCA) and 27,000 controls from the Exome Aggregation Consortium (ExAC) database. Logistic regression was carried out to analyze the association strength (risk) of candidate variants obtained among cases and controls in different populations. Despite the sample size, we detected a significant earlier age of onset in familial TGCT (28y) than sporadic cases (33y), using a Mann–Whitney U test. We identified significant variants in the comparative study of TGCT cases (391) versus controls (almost 1,170), and three of them [PLEC (OR = 6.28, p = 6.42 × 10−23) (p.Arg2016Trp), EXO5 (OR = 3.37, p = 4.82 × 10−09) (p.Arg344AlafsTer10) and DNAH7 (OR = 1.64, p = 0.048)] were replicated as potential candidates that may contribute to explaining the genetic basis of TGCT.
Relation Between Iliopsoas Cross-sectional Area and Kicked Ball Speed in Soccer Players

Abstract This study aimed to investigate the relationship between the maximal anatomical cross-sectional area (ACSA) of the iliopsoas muscle and ball speed in side-foot and instep kicks. The ACSA of the psoas major and iliacus was measured in 29 male collegiate soccer players by using magnetic resonance imaging. They performed maximal side-foot and instep kicks to a stationary ball. The kicked ball speed was measured with a high-speed camera. Ball speed in the side-foot and instep kicks was significantly correlated with body height (side-foot kick: r=0.650, P<0.001; instep kick: r=0.583, P<0.001). After adjustment for body height, the maximal ACSA of the psoas major was significantly correlated with ball speed in the side-foot kick (r=0.441, P=0.017), but not in the instep kick. The maximal ACSA of the iliacus was not correlated with ball speed in side-foot or instep kicks, even after adjustment for body height. Our results suggest that: 1) body height is a significant determinant of the ball speed in side-foot and instep kicks, and 2) for a given body height, the maximal ACSA of the dominant psoas major is a factor that affects the ball speed in side-foot kick.
Diet-Induced Weight Loss Has No Effect on Psychological Stress in Overweight and Obese Adults: A Meta-Analysis of Randomized Controlled Trials

The effect of weight loss on psychological stress is unknown. The study aimed to investigate the effect of diet-induced weight loss in overweight and obese adults on psychological measures of stress through a meta-analysis of randomized controlled trials (RCTs). Databases including Medline Complete, Embase and PsycINFO were searched up to February 2018 for diet-induced weight loss RCTs, which included self-reported assessment of psychological stress. The mean difference between the intervention and control group of changes in stress (intervention—baseline) was used. Ten RCTs were included with 615 participants (502 women, age range 20–80 years). Overall, there was no change in stress (mean difference −0.06, 95% CI: −0.17, 0.06, p = 0.33) and no change in the five studies with a significant reduction in weight in the intervention group compared to a control group that lost no weight (mean difference in weight −3.9 Kg, 95% CI: −5.51, −2.29, p < 0.0001; mean difference in stress 0.04, 95% CI: −0.17, 0.25, p = 0.71). For all analyses, there was low heterogeneity. The benefits of weight loss for those who are overweight and obese do not appear to either increase or reduce psychological stress at the end of the weight loss period.
Model-free functional MRI analysis for detecting low-frequency functional connectivity in the human brain

Slowly varying temporally correlated activity fluctuations between functionally related brain areas have been identified by functional magnetic resonance imaging (fMRI) research in recent years. These low-frequency oscillations of less than 0.08 Hz appear to play a major role in various dynamic functional brain networks, such as the so-called 'default mode' network. They also have been observed as a property of symmetric cortices, and they are known to be present in the motor cortex among others. These low-frequency data are difficult to detect and quantify in fMRI. Traditionally, user-based regions of interests (ROI) or 'seed clusters' have been the primary analysis method. In this paper, we propose unsupervised clustering algorithms based on various distance measures to detect functional connectivity in resting state fMRI. The achieved results are evaluated quantitatively for different distance measures. The Euclidian metric implemented by standard unsupervised clustering approaches is compared with a non-metric topographic mapping of proximities based on the the mutual prediction error between pixel-specific signal dynamics time-series. It is shown that functional connectivity in the motor cortex of the human brain can be detected based on such model-free analysis methods for resting state fMRI.
Automated classification of lymph nodes in USPIO-enhanced MR-images: a comparison of three segmentation methods

Computer assisted detection (CAD) of lymph node metastases may help reduce reading time and improve interpretation of the large amount of image data in an MR-lymphography exam. We compared the influence of using different segmentation methods on the performance of a CAD system for classification of normal and metastasized lymph nodes. Our database consisted of T1 and T2*-weighted pelvic MR images of 603 lymph nodes, enhanced by USPIO contrast medium. For each lymph node, one seed point was manually defined Three automated segmentation methods were compared: 1. Confidence Connected segmentation, extended with automated Bandwidth Factor selection; 2. Conventional Graph Cut segmentation; 3. Pseudo-segmentation by selecting a sphere around the seed point. All lymph nodes were also manually segmented by a radiologist. The resulting segmentations were used to calculate 2 features (mean T1 and T2* signal intensity). Linear discriminant analysis was used for classification. The diagnostic accuracy (AUC at ROC-analysis) was: 0.95 (Confidence- Connected); 0.95 (Graph-Cut); 0.85 (spheres); and 0.95 (manual segmentations). The CAD performance of both the Confidence Connected and Graph Cut methods was as good as the manual segmentation. The substantially lower performance of the sphere segmentations demonstrates the need for accurate segmentations, even in USPIOenhanced images.
Historical Evolution of the Trophic and Limnological Relationships in the Itaipu Reservoir: Top-Down and Bottom-Up Effects upon Fish Production

Many experimental studies have contributed to the development of the theory of trophic chains in lacustrine habitats. They have revealed the important role played by fish, a subject that has been mostly ignored by limnological studies for the past few decades. Most of these studies were developed in Europe and in the United States. The general applicability of this theory has not yet been tested in subtropical and tropical habitats. In spite of controversies, the bottom-up: top-down trophic cascade hypotheses are the most adopted conceptual models. In this context, we examined if these hypotheses may be corroborated by data from the subtropical Itaipu Reservoir. A negative effect was verified between water transparency and total suspended solids. The detritivorous fish exerted a controlling effect on chlorophyll-a concentrations. Bottom-up effects were detected in four trophic levels, and top-down was detected in just one trophic level. The limnological variates influenced the chlorophyll-a concentration, which indicated that the lnTKN plus the effect of the quarter and the reservoir zone (and their interaction) were important.
Detection of Sirtuin-1 protein expression in peripheral blood leukocytes in dogs

Sirtuin-1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylase with a large number of protein substrates. It has attracted a lot of attention in association with extending lifespan. The objective of this study was to enable the evaluation of SIRT1 expression in peripheral blood mononuclear cells (PBMCs) from dogs by flow cytometry. Three transcript variants were amplified from PBMCs by reverse transcription PCR and the nucleotide sequences were analyzed. On the basis of deduced amino acid sequence, a monoclonal antibody against human SIRT1, 1F3, was selected to detect canine SIRT1. Canine SIRT1 in peripheral blood mononuclear cells was successfully detected by western blotting using this antibody. Intracellular canine SIRT1 was also detected in permeabilized 293T cells transfected with a canine SIRT1 expression plasmid by flow cytometry using this antibody. SIRT1 was detected in all leukocyte subsets including lymphocytes, granulocytes and monocytes. The expression level was markedly different among individual dogs. These results indicated that the method applied in this study is useful for evaluating canine SIRT1 levels in PBMCs from dogs.
One-dimensional reduction of viscous jets. I. Theory.

We build a general formalism to describe thin viscous jets as one-dimensional objects with an internal structure. We present in full generality the steps needed to describe the viscous jets around their central line, and we argue that the Taylor expansion of all fields around that line is conveniently expressed in terms of symmetric trace-free tensors living in the two dimensions of the fiber sections. We recover the standard results of axisymmetric jets and we report the first and second corrections to the lowest order description, also allowing for a rotational component around the axis of symmetry. When applied to generally curved fibers, the lowest order description corresponds to a viscous string model whose sections are circular. However, when including the first corrections, we find that curved jets generically develop elliptic sections. Several subtle effects imply that the first corrections cannot be described by a rod model since it amounts to selectively discard some corrections. However, in a fast rotating frame, we find that the dominant effects induced by inertial and Coriolis forces should be correctly described by rod models. For completeness, we also recover the constitutive relations for forces and torques in rod models and exhibit a missing term in the lowest order expression of viscous torque. Given that our method is based on tensors, the complexity of all computations has been beaten down by using an appropriate tensor algebra package such as xAct, allowing us to obtain a one-dimensional description of curved viscous jets with all the first order corrections consistently included. Finally, we find a description for straight fibers with elliptic sections as a special case of these results, and recover that ellipticity is dynamically damped by surface tension. An application to toroidal viscous fibers is presented in the companion paper [Pitrou, Phys. Rev. E 97, 043116 (2018)10.1103/PhysRevE.97. 043116].
Inbreeding, inbreeding depression, and infidelity in a cooperatively breeding bird*

Inbreeding depression plays a major role in shaping mating systems: in particular, inbreeding avoidance is often proposed as a mechanism explaining extra‐pair reproduction in socially monogamous species. This suggestion relies on assumptions that are rarely comprehensively tested: that inbreeding depression is present, that higher kinship between social partners increases infidelity, and that infidelity reduces the frequency of inbreeding. Here, we test these assumptions using 26 years of data for a cooperatively breeding, socially monogamous bird with high female infidelity, the superb fairy‐wren (Malurus cyaneus). Although inbred individuals were rare (∼6% of offspring), we found evidence of inbreeding depression in nestling mass (but not in fledgling survival). Mother–son social pairings resulted in 100% infidelity, but kinship between a social pair did not otherwise predict female infidelity. Nevertheless, extra‐pair offspring were less likely to be inbred than within‐pair offspring. Finally, the social environment (the number of helpers in a group) did not affect offspring inbreeding coefficients or inbreeding depression levels. In conclusion, despite some agreement with the assumptions that are necessary for inbreeding avoidance to drive infidelity, the apparent scarcity of inbreeding events and the observed levels of inbreeding depression seem insufficient to explain the ubiquitous infidelity in this system, beyond the mother–son mating avoidance.
Spatial prior in SVM-based classification of brain images

This paper introduces a general framework for spatial prior in SVM-based classification of brain images based on Laplacian regularization. Most existing methods include spatial prior by adding a feature aggregation step before the SVM classification. The problem of the aggregation step is that the individual information of each feature is lost. Our framework enables to avoid this shortcoming by including the spatial prior directly in the SVM. We demonstrate that this framework can be used to derive embedded regularization corresponding to existing methods for classification of brain images and propose an efficient way to implement them. This framework is illustrated on the classification of MR images from 55 patients with Alzheimer's disease and 82 elderly controls selected from the ADNI database. The results demonstrate that the proposed algorithm enables introducing straightforward and anatomically consistent spatial prior into the classifier.