Miracle-dz/UniFAR-FTUs huggingface dataset:
Forelimb muscle and joint actions in Archosauria: insights from Crocodylus johnstoni (Pseudosuchia) and Mussaurus patagonicus (Sauropodomorpha)

Many of the major locomotor transitions during the evolution of Archosauria, the lineage including crocodiles and birds as well as extinct Dinosauria, were shifts from quadrupedalism to bipedalism (and vice versa). Those occurred within a continuum between more sprawling and erect modes of locomotion and involved drastic changes of limb anatomy and function in several lineages, including sauropodomorph dinosaurs. We present biomechanical computer models of two locomotor extremes within Archosauria in an analysis of joint ranges of motion and the moment arms of the major forelimb muscles in order to quantify biomechanical differences between more sprawling, pseudosuchian (represented the crocodile Crocodylus johnstoni) and more erect, dinosaurian (represented by the sauropodomorph Mussaurus patagonicus) modes of forelimb function. We compare these two locomotor extremes in terms of the reconstructed musculoskeletal anatomy, ranges of motion of the forelimb joints and the moment arm patterns of muscles across those ranges of joint motion. We reconstructed the three-dimensional paths of 30 muscles acting around the shoulder, elbow and wrist joints. We explicitly evaluate how forelimb joint mobility and muscle actions may have changed with postural and anatomical alterations from basal archosaurs to early sauropodomorphs. We thus evaluate in which ways forelimb posture was correlated with muscle leverage, and how such differences fit into a broader evolutionary context (i.e. transition from sprawling quadrupedalism to erect bipedalism and then shifting to graviportal quadrupedalism). Our analysis reveals major differences of muscle actions between the more sprawling and erect models at the shoulder joint. These differences are related not only to the articular surfaces but also to the orientation of the scapula, in which extension/flexion movements in Crocodylus (e.g. protraction of the humerus) correspond to elevation/depression in Mussaurus. Muscle action is highly influenced by limb posture, more so than morphology. Habitual quadrupedalism in Mussaurus is not supported by our analysis of joint range of motion, which indicates that glenohumeral protraction was severely restricted. Additionally, some active pronation of the manus may have been possible in Mussaurus, allowing semi-pronation by a rearranging of the whole antebrachium (not the radius against the ulna, as previously thought) via long-axis rotation at the elbow joint. However, the muscles acting around this joint to actively pronate it may have been too weak to drive or maintain such orientations as opposed to a neutral position in between pronation and supination. Regardless, the origin of quadrupedalism in Sauropoda is not only linked to manus pronation but also to multiple shifts of forelimb morphology, allowing greater flexion movements of the glenohumeral joint and a more columnar forelimb posture.
Comparative Area and Parasitics Analysis in FinFET and Heterojunction Vertical TFET Standard Cells

Vertical tunnel field-effect transistors (VTFETs) have been extensively explored to overcome the scaling limits and to improve on-current (ION) compared to standard lateral device structures for the future technologies. The benefits in terms of reduced footprint, high ION and feasibility of fabrication have been demonstrated in several works. Among various VTFETs, the asymmetric heterojunction vertical tunnel FETs (HVTFETs) have emerged as one of the promising alternatives to standard transistors for low-voltage applications. However, while such device-level benefits without parasitics have been widely investigated, logic-gate design with parasitics and layout implications are not clear. In this article, we investigate and compare the layouts and parasitic capacitances and resistances of HVTFETs with FinFETs. Due to the vertical device structure of HVTFETs, a smaller footprint is observed compared to FinFETs in cells with small fan-in. However, for high fan-in cells, HVTFETs exhibit area overheads due to infeasibility of contact sharing in parallel and series transistors. These area overheads also lead to approximately 48% higher parasitic capacitance and resistance compared to FinFETs when the number of parallel and series connections increases. Further, in order to analyze the impact of parasitics, we modeled the analytical parasitics in SPICE. The models for both HVTFETs and FinFETs with parasitics were used to simulate a 15-stage inverter-based ring oscillator (RO) in order to compare the delay and energy. Our simulation results clearly show that HVTFETs exhibit less delay at a VDD < 0.45 V and higher energy efficiency for VDDs in the range of 0.3V--0.7V, albeit at the cost of 8% performance degradation.
Coordinating Crowd-Sourced Services

The growing ubiquity of smartphones and similar personal connected computational devices, each with a number of sensors, has created an opportunity for useful services based on crowd-sourced data. A busy professional could find a restaurant to go to for a quick lunch based on information available from smartphones of people already there having lunch, waiting to be seated, or even heading there, a government could conduct a census in real-time, or "sense" public opinion. Although the programming required for offering a new service of this sort can be significant if done from scratch, these applications have something in common: they use a similar pattern of coordinated communications between the various parties. This creates an opportunity to offer a set of coordination mechanisms as a platform to service designers, into which they can simply plug in their service specific code to offer a new service. This paper identifies the coordination mechanisms required for these crowd-sourced services as types of multi-origin communication. We present details of how these core mechanisms can be implemented using Actors, and introduce high-level programming constructs for launching a new service. Finally, we use examples to illustrate the implementation of services.
Inhibition of histone deacetylase activity induces developmental plasticity in oligodendrocyte precursor cells

Recently, it was demonstrated that lineage-committed oligodendrocyte precursor cells (OPCs) can be converted to multipotent neural stem-like cells, capable of generating both neurons and glia after exposure to bone morphogenetic proteins. In an effort to understand and control the developmental plasticity of OPCs, we developed a high-throughput screen to identify novel chemical inducers of OPC reprogramming. Using this system, we discovered that inhibition of histone deacetylase (HDAC) activity in OPCs acts as a priming event in the induction of developmental plasticity, thereby expanding the differentiation potential to include the neuronal lineage. This conversion was found to be mediated, in part, through reactivation of sox2 and was highly reproducible at the clonal level. Further, genome-wide expression analysis demonstrated that HDAC inhibitor treatment activated sox2 and 12 other genes that identify or maintain the neural stem cell state while simultaneously silencing a large group of oligodendrocyte lineage-specific genes. This series of experiments demonstrates that global histone acetylation, induced by HDAC inhibition, can partially reverse the lineage restriction of OPCs, thereby inducing developmental plasticity.
Superfluid density and specific heat within a self-consistent scheme for a two-band superconductor

The two gaps in a two-band clean $s$-wave superconductor are evaluated self-consistently within the quasiclassical Eilenberger weak-coupling formalism with two in-band and one interband pairing potentials. Superfluid density, free energy, and specific heat are given in the form amenable for fitting the experimental data. Well-known two-band ${\text{MgB}}_{2}$ and ${\text{V}}_{3}\text{Si}$ superconductors are used to test the developed approach. The pairing potentials obtained from the fit of the superfluid density data in ${\text{MgB}}_{2}$ crystal were used to calculate temperature-dependent specific heat $C(T)$. The calculated $C(T)$ compares well with the experimental data. Advantages and validity of this, which we call the ``$\ensuremath{\gamma}$ model,'' are discussed and compared with the commonly used empirical (and not self-consistent) ``$\ensuremath{\alpha}$ model. '' Correlation between the sign of the interband coupling and the signs of the two order parameters is discussed. Suppression of the critical temperature by the interband scattering is evaluated and shown to be severe for the interband repulsion as compared to the attraction. The data on a strong ${T}_{c}$ suppression in ${\text{MgB}}_{2}$ crystals by impurities suggest that the order parameters on two effective bands of this material may have opposite signs, i.e., may have the ${s}_{\ifmmode\pm\else\textpm\fi{}}$ structure similar to proposals for iron-based pnictide superconductors.
Emerging Roles of the Mineralocorticoid Receptor in Pathology: Toward New Paradigms in Clinical Pharmacology

The mineralocorticoid receptor (MR) and its ligand aldosterone are the principal modulators of hormone-regulated renal sodium reabsorption. In addition to the kidney, there are several other cells and organs expressing MR, in which its activation mediates pathologic changes, indicating potential therapeutic applications of pharmacological MR antagonism. Steroidal MR antagonists have been used for decades to fight hypertension and more recently heart failure. New therapeutic indications are now arising, and nonsteroidal MR antagonists are currently under development. This review is focused on nonclassic MR targets in cardiac, vascular, renal, metabolic, ocular, and cutaneous diseases. The MR, associated with other risk factors, is involved in organ fibrosis, inflammation, oxidative stress, and aging; for example, in the kidney and heart MR mediates hormonal tissue-specific ion channel regulation. Genetic and epigenetic modifications of MR expression/activity that have been documented in hypertension may also present significant risk factors in other diseases and be susceptible to MR antagonism. Excess mineralocorticoid signaling, mediated by aldosterone or glucocorticoids binding, now appears deleterious in the progression of pathologies that may lead to end-stage organ failure and could therefore benefit from the repositioning of pharmacological MR antagonists.
Location of Repetitive Regions in Sequences By Optimizing A Compression Method

Suppose that a biologist wishes to study some local property P of genetic sequences. If he can design (with a computer scientist) an algorithm C which efficiently compresses parts of the sequence which satisfy P, then our algorithm TurboOptLift locates very quickly where property P occurs by chance on a sequence, and where it occurs as a result of a significant process. Under some conditions, the time complexity of TurboOptLift is O(n log n). We illustrate its use on the practical problem of locating approximate tandem repeats in DNA sequences.
A Meta-Analysis of Socio-Demographic Factors for Perinatal Mortality in Developing Countries: A Subgroup Analysis of the National Surveys and Small Scale Studies

Background Although the perinatal mortality in low income countries is about five-folds higher than in the high income countries, little is known about the association of socio-demographic factors with perinatal mortality. National and small scale studies so far reported have shown very contradictory results. The objective of this meta-analysis was to assess the association of perinatal mortality with selected sociodemographic factors. Methods A computer based literature search was conducted mainly in the databases of African Journals Online, MEASURE Demographic and Health Survey (DHS), Google Scholar, HINARI, PUBMED, MEDLINE and the Cochrane Library. The inclusion criteria were: 1) studies that assessed the perinatal mortality in developing countries in relation to socio-demographic predictors and 2) studies published in English and conducted after the year 1990. Subgroup meta-analyses of perinatal mortality were performed for mothers' age, residence, educational level and wealth status. Sensitivity analysis and heterogeneity testing were done. Results In this meta-analysis, several inconsistent associations of perinatal mortality with the selected socio-demographic variables were observed in the primary studies level, both DHS and small scale studies. However, the overall odds ratio (OR) demonstrated statistically significant association of perinatal mortality with low maternal age (OR=1.2) and short birth interval (OR=1.4) but was not influenced by the mothers' residence, low educational level and household wealth index. Very consistently, the highest perinatal mortality rates reported when the birth intervals were either too short (<15 months) or too long (>39 months). Conclusion Because of the disagreement among previous studies, the present study demonstrated a small effect size on the increased risk of perinatal mortality among women who were pregnant during teenage ages and gave birth too frequently or after a long interval. Therefore, to confirm the strong predictors of perinatal mortality, further studies on sociodemographic factors are needed.
Extracting opinion explanations from Chinese online reviews

Opinion mining has gained increasing attention and shown great practical value in recent years. Existing research on opinion mining mainly focuses on the extraction of lexicon orientation and opinion targets. The explanations of opinions, which are potentially valuable for many applications, are totally ignored. To address this specific research challenge, in this paper, we propose an approach to extract the explanation of reason and/or consequence behind an opinion via learning word pairs and using causal indicators from Chinese online reviews. We also improve our word pair based method by constructing clusters of word paris. Experiments on a Chinese business review corpus show that our method is feasible and effective.
Effect of rounding on the sensitivity of optical antennas based sensors

In this work we present the effect of rounding on the bulk sensitivity of the optical antenna. Dipole structures are simulated. Fabrication of the dipole optical antenna structures involves use of high resolution e-beam lithography (EBL), metal deposition and lift-off. It is expected that using the fabrication process, we should be able to fabricate exact dipole structures with sharp corners without using any advanced techniques like proximity corrections etc. These techniques increase the cost of the device. So, it is important to determine that whether the rounded corners improve the sensitivity for the sensors. Using Finite Difference Time Domain (FDTD) simulation techniques we found that dipole structure with rounded corners improves the sensitivity of the gas sensor.
Dominant Cross-Reactive B Cell Response during Secondary Acute Dengue Virus Infection in Humans

The four serotypes of dengue virus (DENV) cause dengue fever (DF) and dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Severe disease has been associated with heterotypic secondary DENV infection, mediated by cross-reactive antibodies (Abs) and/or cross-reactive T cells. The role of cross-reactive immunity in mediating enhanced disease versus cross-protection against secondary heterotypic DENV infection is not well defined. A better understanding of the cross-reactive immune response in natural infections is critical for development of safe and effective tetravalent vaccines. We studied the B cell phenotype of circulating B cells in the blood of pediatric patients suspected of dengue during the 2010–2011 dengue season in Managua, Nicaragua (n = 216), which was dominated by the DENV-3 serotype. We found a markedly larger percentage of plasmablast/plasma cells (PB/PCs) circulating in DENV-positive patients as compared to patients with Other Febrile Illnesses (OFIs). The percentage of DENV-specific PB/PCs against DENV-3 represented 10% of the circulating antibody-producing cells (ASCs) in secondary DENV-3 infections. Importantly, the cross-reactive DENV-specific B cell response was higher against a heterotypic serotype, with 46% of circulating PB/PCs specific to DENV-2 and 10% specific to DENV-3 during acute infection. We also observed a higher cross-reactive DENV-specific IgG serum avidity directed against DENV-2 as compared to DENV-3 during acute infection. The neutralization capacity of the serum was broadly cross-reactive against the four DENV serotypes both during the acute phase and at 3 months post-onset of symptoms. Overall, the cross-reactive B cell immune response dominates during secondary DENV infections in humans. These results reflect our recent findings in a mouse model of DENV cross-protection. In addition, this study enabled the development of increased technical and research capacity of Nicaraguan scientists and the implementation of several new immunological assays in the field.
Bayesian Scale Estimation for Monocular SLAM Based on Generic Object Detection for Correcting Scale Drift

We propose a novel real-time algorithm for estimating the local scale correction of a monocular SLAM system, to obtain a correctly scaled version of the 3D map and of the camera trajectory. Within a Bayesian framework, it integrates observations from a deep-learning based generic object detector and landmarks from the map whose projection lie inside a detection region, to produce scale correction estimates from single frames. For each observation, a prior distribution on the height of the detected object class is used to define the observation's likelihood. Due to the scale drift inherent to monocular SLAM systems, we also incorporate a rough model on the dynamics of scale drift. Quantitative evaluations are presented on the KITTI dataset, and compared with different approaches. The results show a superior performance of our proposal in terms of relative translational error when compared to other monocular systems based on object detection.
Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays

Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, but differences in CNV call thresholds and characteristics exist. We evaluated the relative performance of seven methods: circular binary segmentation, CNVFinder, cnvPartition, gain and loss of DNA, Nexus algorithms, PennCNV and QuantiSNP. Tested data included real and simulated Illumina HumHap 550 data from the Singapore cohort study of the risk factors for Myopia (SCORM) and simulated data from Affymetrix 6.0 and platform-independent distributions. The normalized singleton ratio (NSR) is proposed as a metric for parameter optimization before enacting full analysis. We used 10 SCORM samples for optimizing parameter settings for each method and then evaluated method performance at optimal parameters using 100 SCORM samples. The statistical power, false positive rates, and receiver operating characteristic (ROC) curve residuals were evaluated by simulation studies. Optimal parameters, as determined by NSR and ROC curve residuals, were consistent across datasets. QuantiSNP outperformed other methods based on ROC curve residuals over most datasets. Nexus Rank and SNPRank have low specificity and high power. Nexus Rank calls oversized CNVs. PennCNV detects one of the fewest numbers of CNVs.
Determinants of Target Capital Structure: The Case of Dual Debt and Equity Issues

We examine whether market and operating performance affect corporate financing behavior because they are related to target leverage. Our focus on firms that issue both debt and equity enhances our ability to draw inferences. Consistent with dynamic tradeoff theories, dual issuers offset the deviation from the target resulting from accumulation of earnings and losses. Our results also imply that high market-to-book firms have low target debt ratios. On the other hand, consistent with market timing, high stock returns increase the probability of equity issuance, but have no effect on target leverage.
Streptococcus oligofermentans inhibits Streptococcus mutans through conversion of lactic acid into inhibitory H2O2: a possible counteroffensive strategy for interspecies competition

The oral microbial flora contains over 500 different microbial species that often interact as a means to compete for limited space and nutritional resources. Streptococcus mutans, a major caries‐causing pathogen, is a species which tends to interact competitively with other species in the oral cavity, largely due to its ability to generate copious quantities of the toxic metabolite, lactic acid. However, during a recent clinical study, we discovered a novel oral streptococcal species, Streptococcus oligofermentans, whose abundance appeared to be inversely correlated with that of S. mutans within dental plaque samples and thus suggested a possible antagonistic relationship with S. mutans. In this study, we used a defined in vitro interspecies interaction assay to confirm that S. oligofermentans was indeed able to inhibit the growth of S. mutans. Interestingly, this inhibitory effect was relatively specific to S. mutans and was actually enhanced by the presence of lactic acid. Biochemical analyses revealed that S. oligofermentans inhibited the growth of S. mutans via the production of hydrogen peroxide with lactic acid as the substrate. Further genetic and molecular analysis led to the discovery of the lactate oxidase (lox) gene of S. oligofermentans as responsible for this biological activity. Consequently, the lox mutant of S. oligofermentans also showed dramatically reduced inhibitory effects against S. mutans and also exhibited greatly impaired growth in the presence of the lactate produced by S. mutans. These data indicate that S. oligofermentans possesses the capacity to convert its competitor's main ‘weapon’ (lactic acid) into an inhibitory chemical (H2O2) in order to gain a competitive growth advantage. This fascinating ability may be an example of a counteroffensive strategy used during chemical warfare within the oral microbial community.