Miracle-dz/UniFAR-FTUs huggingface dataset:
Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

ABSTRACT Objectives Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700‐year‐old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in‐solution capture techniques, followed by Illumina high‐throughput sequencing. Results Full mitogenomes (7–34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220–228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
The effect of spermine on the disaccharidase activities in suckling rats of different age.

The influence of the age of the rat on the maturation of disaccharidase activities induced by spermine was studied. Three‐day‐ and 9‐day‐old rats were used in the experiment. Spermine was administered orally or directly into the stomach using thin tubing daily for 3 days, and disaccharidase activities in the jejunum were measured. While spermine caused maturation of not only lactase activity but also maltase and sucrase activities in 9‐day‐old rats, it only caused maturation of lactase activity in 3‐day‐old rats. Histological studies showed no significant changes in the jejunum of 3‐day‐old rats treated with spermine.
Registration and Comparison of Facial Images in Different Matching Algorithms Hemamalini G E 1 and

In computer vision robust feature detection, image matching are the latest concepts that most of the researchers have carried out in this field. Face recognition is also an important field of research. It is also considered one of the most prolific forms of biometrics. The personal identity based on geometric or statistical feature derived from face images are automatically recognised. This paper proposes various methods and algorithms used for face recognition and registration such as SIFT, SURF and FAST AFFINE. Feature extraction and feature matching are the steps of image registration and the accuracy of image registration depends on feature matching. SIFT is a proposal method commonly used in face recognition. In order to overcome the drawback of SIFT a new detector and descriptor SURF is used as improved form of SIFT. In this paper an attempt is made to review various method used for face recognition and registration. ASIFT, SURF & FAST AFFINE are the methods used for feature matching. RANSAC is used for outlier detection method and at the end; affine transformation is used as a transformation model for image registration. Comparison of these methods is done and performance is seen on the basis of recognition rate. The results obtained exhibits that the ASIFT algorithm method outperforms the other methods based on accuracy and computation time. Keyword: SIFT, SURF, FASF, Affine transform, and RANSAC.
Topologically Protected AC Transport Induced by Spin–Orbit Interaction in H-Shaped Silicene Nanojunction

The linear ac transport properties are theoretically studied in H-shaped zigzag silicene nanojunction. We numerically calculated the dc conductance and ac emittance by considering the nearest-neighbor hopping, the second-nearest-neighbor spin–orbit interaction (SOI), and external electric field, based on the tight-binding approach and the ac transport theory. It is found that the relatively large SOI induces a topological quantum edge state in the nanojunction, which eliminates the ac emittance response at the Dirac point. Further investigations indicate that the SOI-induced ac transport is topologically protected, despite the changes of geometric size. Moreover, the external electric field would open an energy gap, and destroy the topological quantum state, making the nanojunction a trivial band insulator.
The relationship between nighttime hypertension and left atrial function

The authors sought to investigate the association between different hypertensive phenotypes and left atrial (LA) function assessed by the volumetric method and the strain method in patients with untreated hypertension. This cross‐sectional study involved 236 untreated patients who underwent 24‐hour ambulatory blood pressure monitoring and two‐dimensional echocardiographic examination. Our findings showed that LA function gradually deteriorated from patients with normotension, across patients with daytime hypertension, to patients with night‐ and day‐nighttime hypertension. LA reservoir and conduit functions were particularly deteriorated in patients with nighttime and day‐nighttime hypertension compared with patients with normotension and patients with daytime hypertension, whereas LA pump function was compensatorily increased only in the participants with day‐nighttime hypertension. Only nighttime hypertension and day‐nighttime hypertension were independently associated with the reduced reservoir and conduit LA function. The difference between patients with daytime and nighttime hypertension was found in reservoir and conduit LA but not LA pump function.
Survival and Heat Resistance of Salmonella enterica and Escherichia coli O157:H7 in Peanut Butter

ABSTRACT Significant differences (P < 0.05) were found between the survival rates of Salmonella enterica and Escherichia coli O157:H7 in peanut butter with different formulations and water activity. High carbohydrate content in peanut butter and low incubation temperature resulted in higher levels of bacterial survival during storage but lower levels of bacterial resistance to heat treatment.
Exponential stability of multiple equilibria for memristive Cohen-Grossberg neural networks with non-monotonic activation functions

This paper is concerned with the problem of exponential stability of multiple equilibria for memristive Cohen-Grossberg neural networks with non-monotonic piece-wise linear activation functions. First, the fixed point theorem and nonsmooth analysis theory are applied to develop some sufficient conditions under which n-dimensional memristive Cohen-Grossberg neural networks with non-monotonic activation functions are ensured to have 5n equilibrium points. Then, with the aid of the theories of set-valued maps and differential inclusions, the exponential stability is proved for 3n equilibrium points out of those 5n equilibrium points. The importance of the multistability results obtained in this paper lies in that the use of the proposed non-monotonic activation functions can increase the storage capacity of the corresponding neural networks considerably.
A Quest for Exactness: Program Transformation for Reliable Real Numbers. (Transformation de Programmes pour des Nombres Réels Fiables)

This thesis presents an algorithm that eliminates square root and division operations in some straight-line programs used in embedded systems while preserving the semantics. Eliminating these two operations allows to avoid errors at runtime due to rounding. These errors can lead to a completely unexpected behavior from the program. This transformation respects the constraints of embedded systems, such as the need for the program to be executed in a fixed size memory. The transformation uses two fundamental algorithms developed in this thesis. The first one allows to eliminate square roots and divisions from Boolean expressions built with comparisons of arithmetic expressions. The second one is an algorithm that solves a particular anti-unification problem, that we call constrained anti-unification. This program transformation is defined and proven in the PVS proof assistant. It is also implemented as a strategy for this system. Con- strained anti-unification is also used to extend this transformation to programs containing functions. It allows to eliminate square roots and divisions from PVS specifications. Robustness of this method is highlighted by a major example: the elimination of square roots and divisions in a conflict detection algorithm used in aeronautics.
Integration of Nanoscale Science and Technology into Undergraduate Curricula

An interdisciplinary group at the University of Cincinnati was recently awarded an NSF Nanotechnology Undergraduate Education grant, Integration of Nanoscale Science and Engineering into Undergraduate Curricula. The faculty come from Engineering, Physics, Chemistry, and Philosophy departments. The overall goal of this project is to incorporate nanotechnology education into undergraduate curricula in the Colleges of Engineering and Arts & Sciences. This paper will discuss the material taught in the two courses and the reaction of the students to highly interdisciplinary team teaching of nanotechnology. The lectures provide an overview of nanoscale science and engineering, with applications in nanomaterials, nanophotonics, nanoelectronics, nanomechanics, and bionanosystems. We also include lectures on societal and ethical implications of the nanoscale. The laboratory modules give students hands-on experience including synthesis of nanoparticles and nanotubes, and subsequent characterization with multiple stations of atomic force microscopes and laser spectrometers.
The Role of Religious Involvement in Black-White Differences in Alcohol Use Disorders.

OBJECTIVE To date, a paradox in the social epidemiology of alcohol use disorders (AUDs) remains unresolved: non-Hispanic Blacks experience higher socioeconomic disadvantage, stressor exposures, and individual stress-prominent AUD risk factors, yet have lower than expected AUD risk compared with non-Hispanic Whites. Religious involvement is associated with lower AUD risk. Non-Hispanic Blacks are highly religiously involved. Together, those facts may account for Black-White differences in AUD risk. METHOD We used Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) (N = 26,784) to examine whether (a) religious involvement accounts for Black-White differences in AUD risk, and (b) race moderates the association between religious involvement and AUD. Religious involvement indicators were service attendance, social interaction, and subjective religiosity and spirituality. Twelve-month AUD prevalence as defined by the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, was the outcome. Covariates were age, education, income, marital status, and U.S.-born versus foreign-born nativity. RESULTS Blacks were significantly less likely than Whites to have an AUD (adjusted odds ratio [aOR] for men = 0.70, 95% CI [0.59, 0.83]; aOR for women = 0.71, 95% CI [0.57, 0.89]). An adjusted model with all three religious involvement indicators explained 17% of race differences among men (OR = 0.82) and 45% among women (OR = 1.03). There was no evidence that the association between religious involvement and AUD differed between Blacks and Whites. CONCLUSIONS Religious service attendance, subjective religiosity, and spirituality account for a meaningful share of the Black-White differences in AUD. Future research is needed to conduct more fine-grained analyses of the aspects of religious involvement that are potentially protective against AUD, ideally differentiating between social norms associated with religious involvement, social support offered by religious participation, and deeply personal aspects of spirituality.
Reversal of the decision for caesarean section in the second stage of labour on the basis of consultant vaginal assessment

During a 5-year period there were 32 cases where the vaginal assessment performed by a specialist registrar in the second stage of labour was re-assessed within 15 minutes by a consultant obstetrician. The examination was prompted by a request for permission to perform a caesarean section in the second stage of labour. The results suggest a significant discrepancy between the consultants and the specialist registrar's findings, with 44% of the cases indicating a difference in the position of the head, and 81% a difference in the station of the head. No comment was made about caput or moulding in the majority of cases (94%). The study findings suggest that vaginal examination, like instrumental delivery, is a skill that is being eroded and will require formal instruction to address this problem.
Theory and Simulations of a Conformal Omni- Directional Subwavelength Metamaterial Leaky-Wave Antenna

The detailed theory of a single subwavelength conformal radiator that exploits the resonant properties of thin cylindrical metamaterial shells supporting leaky waves is presented. It is shown and reviewed analytically and numerically how a circularly symmetric resonant leaky mode may be supported by a properly designed subwavelength homogenous cylindrical shell of low negative permittivity. Some physical insights are provided and numerical simulations with a feed point, considering also the finite-ness of the antenna in the longitudinal direction, are presented and discussed. Moreover, possibilities and limitations of a practical realization of this setup are mentioned, considering in details the possible anisotropies in the metamaterials.
Synthetic Cationic Peptide IDR-1002 Provides Protection against Bacterial Infections through Chemokine Induction and Enhanced Leukocyte Recruitment

With the rapid rise in the incidence of multidrug resistant infections, there is substantial interest in host defense peptides as templates for production of new antimicrobial therapeutics. Natural peptides are multifunctional mediators of the innate immune response, with some direct antimicrobial activity and diverse immunomodulatory properties. We have previously developed an innate defense regulator (IDR) 1, with protective activity against bacterial infection mediated entirely through its effects on the immunity of the host, as a novel approach to anti-infective therapy. In this study, an immunomodulatory peptide IDR-1002 was selected from a library of bactenecin derivatives based on its substantially more potent ability to induce chemokines in human PBMCs. The enhanced chemokine induction activity of the peptide in vitro correlated with stronger protective activity in vivo in the Staphylococcus aureus-invasive infection model, with a >5-fold reduction in the protective dose in direct comparison with IDR-1. IDR-1002 also afforded protection against the Gram-negative bacterial pathogen Escherichia coli. Chemokine induction by IDR-1002 was found to be mediated through a Gi-coupled receptor and the PI3K, NF-κB, and MAPK signaling pathways. The protective activity of the peptide was associated with in vivo augmentation of chemokine production and recruitment of neutrophils and monocytes to the site of infection. These results highlight the importance of the chemokine induction activity of host defense peptides and demonstrate that the optimization of the ex vivo chemokine-induction properties of peptides is a promising method for the rational development of immunomodulatory IDR peptides with enhanced anti-infective activity.
CHARACTERIZATION OF LOW SALT STRESS INDUCED ALTERATIONS IN THE PHOTOSYNTHETIC ELECTRON TRANSPORT IN SPIRULINA PLATENSIS

In this investigation an attempt has been made to characterize the alterations in photosynthetic parameters by depriving salt (NaCl) from the growth medium of the cyanobacterium Spirulina platensis and also by re-addition of salt after different intervals (0-42 min). Salt deprivation primarily affected the photosystem (PS) II catalysed electron transport. Most probably due to the alterations in water oxidation complex could be responsible for the altered PS II photochemistry. Experiments related to the re-addition of salt also suggested the recovery of the loss in PS II activity after 42 min of incubation. Fluorescence kinetic measurements made by pulse amplitude modulator (PAM) kinetic fluorimeter also supported the above observation in the above cyanobacterium.
Studying Stability of Different Convolutional Neural Networks Against Additive Noise

Understanding internal process of ConvNets is commonly done using visualization techniques. However, these techniques do not usually provide a tool for estimating stability of a ConvNet against noise. In this paper, we show how to analyze a ConvNet in the frequency domain. Using the frequency domain analysis, we show the reason that a ConvNet might be sensitive to a very low magnitude additive noise. Our experiments on a few ConvNets trained on different datasets reveals that convolution kernels of a trained ConvNet usually pass most of the frequencies and they are not able to effectively eliminate the effect of high frequencies.They also show that a convolution kernel with more concentrated frequency response is more stable against noise. Finally, we illustrate that augmenting a dataset with noisy images can compress the frequency response of convolution
Fas‐mediated T‐cell apoptosis is impaired in patients with chronic inflammatory demyelinating polyneuropathy

Abstract The Fas death receptor is expressed by activated lymphocytes and is involved in switching‐off the immune response. Its inherited defects cause auto‐immune lymphoproliferative syndrome. Impaired Fas function may also play a role in other auto‐immune diseases, such as multiple sclerosis and type 1 diabetes mellitus. The aim of this work was to evaluate Fas function in T cells from patients with chronic inflammatory demyelinating polyneuropathy (CIDP). We evaluated Fas‐induced apoptosis in T‐cell lines from 27 patients with CIDP, 12 patients with acute inflammatory demyelinating polyneuropathy (AIDP), and 110 controls. CIDP patients displayed lower Fas function than both AIDP patients and controls, whereas no statistically significant difference was found between AIDP patients and controls. Moreover, Fas function was lower in CIDP patients with progressive course than in those with relapsing–remitting course and lower in CIDP patients with axonal damage than in those with pure demyelination. These data suggest that defective Fas function favours CIDP development and aggressive evolution.
Apatites in lunar KREEP basalts: The missing link to understanding the H isotope systematics of the Moon

Recent re-analyses of lunar samples have undoubtedly measured indigenous water, challenging the paradigm of a “dry” Moon, and arguing that some portions of the lunar interior are as wet as some regions of the Earth’s mantle and that water in both planetary bodies likely share a common origin. Mare basalts indirectly sample the lunar mantle and are affected by petrogenetic processes such as crystallization and degassing that can modify characteristics of indigenous water in primary mantle melts. Analyses of apatite in phosphorus-rich KREEP (K + REE [rare earth elements] + P) basalts may provide more reliable estimates for the water content of lunar magmas, as some apatites likely crystallized before substantial degassing occurred. In lunar KREEP basalt sample 15386, apatite H 2 O content and H isotopic composition suggest that degassing occurred during apatite crystallization, the lowest δD value of 90‰ ± 100‰ representing an upper limit for the isotopic composition of water in the parental magma. Interpretation of the data for KREEP basalt 15386 suggests that this basalt is characterized by relatively elevated H 2 O contents and CI chondrite–type δD values, similar to those proposed for other mare basalts and pyroclastic glasses. On the other hand, most of the apatites in lunar KREEP basalt 72275 and lunar meteorite NWA 773 crystallized before degassing and H isotope fractionation, and their D/H ratios thus directly refl ect those of their source regions. These apatites have an average δD value of –130‰ ± 50‰, suggesting the presence of a water reservoir in the Moon characterized by moderate H 2 O contents and H isotopic composition similar to that of Earth’s interior. These fi ndings imply that signifi cant amounts of water in the Moon were inherited from the proto-Earth, surviving the purported Moon-forming impact event.
Distinct epigenetic shift in a subset of Glioma CpG island methylator phenotype (G-CIMP) during tumor recurrence

Histomorphology and current grading schemes are unable to predict glioma relapse and malignant tumor progression. We reported that the IDH-mutant associated Glioma-CpG Island Methylator Phenotype (G-CIMP) can be further divided into two clinically distinct subtypes independent of histopathological grading (G-CIMP-high and -low) with evidence of correlation with tumor progression. Here we performed a comprehensive epigenomic analysis of 74 longitudinally collected glioma samples (grade II-IV) to understand malignant recurrence from G-CIMP-high to G-CIMP-low. G-CIMP-low recurrence appeared in 12% of all gliomas and resemble IDH-wildtype primary glioblastoma. G-CIMP-low recurrence can be characterized by distinct epigenetic changes at candidate functional tissue enhancers with AP-1/SOX binding elements, stem cell-like epigenomic phenotype, and genomic instability. Finally, we defined a set of candidate biomarker signatures that predict recurrence of G-CIMP-low with clinically relevance on patient outcomes. Our study provides opportunity for refined clinical trial designs and therapeutic targets that limit progression to more aggressive G-CIMP-low phenotype. HIGHLIGHTS Indolent G-CIMP-high progresses to aggressive G-CIMP-low phenotype Incidence of G-CIMP-low recurrent tumors are 3 times greater than G-CIMP-low primary G-CIMP-low recurrent tumors share epigenomic features with IDH-wildtype primary GBM Predictive biomarkers of G-CIMP-low progression at primary diagnosis