Miracle-dz/UniFAR-FTUs huggingface dataset:
Global DNA Hypermethylation in Down Syndrome Placenta

Down syndrome (DS), commonly caused by an extra copy of chromosome 21 (chr21), occurs in approximately one out of 700 live births. Precisely how an extra chr21 causes over 80 clinically defined phenotypes is not yet clear. Reduced representation bisulfite sequencing (RRBS) analysis at single base resolution revealed DNA hypermethylation in all autosomes in DS samples. We hypothesize that such global hypermethylation may be mediated by down-regulation of TET family genes involved in DNA demethylation, and down-regulation of REST/NRSF involved in transcriptional and epigenetic regulation. Genes located on chr21 were up-regulated by an average of 53% in DS compared to normal villi, while genes with promoter hypermethylation were modestly down-regulated. DNA methylation perturbation was conserved in DS placenta villi and in adult DS peripheral blood leukocytes, and enriched for genes known to be causally associated with DS phenotypes. Our data suggest that global epigenetic changes may occur early in development and contribute to DS phenotypes.
Identification of a novel folate receptor, a truncated receptor, and receptor type beta in hematopoietic cells: cDNA cloning, expression, immunoreactivity, and tissue specificity.

The expression of a membrane-associated folate receptor (FR) was elevated in spleen samples from patients with chronic (CML) and acute (AML) myelogenous leukemias compared with normal spleen. Contrary to earlier reports, antibodies to a purified FR from placenta cross-reacted quantitatively with this protein in solution radioimmunoassays. Similar to FR-alpha (KB cells) and FR-beta (placenta), the protein was released from the membrane by phosphatidylinositol-specific phospholipase C, indicating a glycosylphosphatidylinositol (GPI) membrane anchor. Screening of a cDNA library from CML spleen with a heterologous murine FR cDNA and also amplification of FR cDNAs from spleen and bone marrow in CML, AML, chronic lymphocytic leukemia (CLL), and acute lymphocytic leukemia (ALL) by polymerase chain reaction (PCR) using degenerate oligonucleotides yielded cDNA clones representing FR-beta, a novel FR (type gamma), and an aberrant transcript of FR-gamma with a 2 base pair deletion resulting in a truncated 104-residue polypeptide; FR-alpha was not detected in these tissues. The cDNA for FR-gamma predicts a 243-residue polypeptide with an amino acid sequence homology of 71% and 79% with FR-alpha and FR-beta, respectively, a 23-residue amino-terminal signal peptide, and 3 potential sites for N-linked glycosylation. Transfection of COS-1 cells with the cDNA for FR-gamma resulted in low expression of a [3H]folic acid binding protein on the cell surface that was GPI-anchored. PCR analysis of total RNA from a number of normal and malignant tissues and cell lines indicated a limited tissue specificity of FR-gamma. (ABSTRACT TRUNCATED AT 250 WORDS)
Optimization and analysis of distributed averaging with memory

This paper analyzes the rate of convergence of a distributed averaging scheme making use of memory at each node. In conventional distributed averaging, each node computes an update based on its current state and the current states of their neighbours. Previous work observed the trajectories at each node converge smoothly and demonstrated via simulation that a predictive framework can lead to faster rates of convergence. This paper provides theoretical guarantees for a distributed averaging algorithm with memory. We analyze a scheme where updates are computed as a convex combination of two terms: (i) the usual update using only current states, and (ii) a local linear predictor term that makes use of a node's current and previous states. Although this scheme only requires one additional memory register, we prove that this approach can lead to dramatic improvements in the rate of convergence. For example, on the N-node chain topology, our approach leads to a factor of N improvement over the standard approach, and on the two-dimensional grid, our approach achieves a factor of √N improvement. Our analysis is direct and involves relating the eigenvalues of a conventional (memoryless) averaging matrix to the eigenvalues of the averaging matrix implementing the proposed scheme via a standard linearization of the quadratic eigenvalue problem. The success of our approach relies on each node using the optimal parameter for combining the two update terms. We derive a closed form expression for the optimal parameter as a function of the second largest eigenvalue of a memoryless averaging matrix, which can easily be computed in a decentralized fashion using existing methods, making our approach amenable to a practical implementation.
Dynamic range compression by differential zone mapping based on psychophysical experiments

In this paper we present a new technique for the display of High Dynamic Range (HDR) images on Low Dynamic Range (LDR) displays. The described process has three stages. First, the input image is segmented into luminance zones. Second, the tone mapping operator (TMO) that performs better in each zone is automatically selected. Finally, the resulting tone mapping (TM) outputs for each zone are merged, generating the final LDR output image. To establish the TMO that performs better in each luminance zone we conducted a preliminary psychophysical experiment using a set of HDR images and six different TMOs. We validated our composite technique on several (new) HDR images and conducted a further psychophysical experiment, using an HDR display as reference, that establishes the advantages of our hybrid three-stage approach over a traditional individual TMO.
Does Remediation Work for All Students? How the Effects of Postsecondary Remedial and Developmental Courses Vary by Level of Academic Preparation

We examine the impact of remedial and developmental courses on college students with varying levels of academic preparedness, thus focusing on a wider range of students than previous studies. Using a regression discontinuity design, we provide causal estimates of the effects of placement in different levels of remedial courses on short-, intermediate-, and long-term outcomes at both 2- and 4-year colleges. Similar to other research, we find that remediation has negative effects for students on the margin of needing one developmental course. However, for students with lower levels of academic preparation, the effects of remediation are estimated to be positive in some subjects. These results suggest that remedial courses can help or hinder students differently depending on their incoming levels of academic preparedness. Moreover, our conclusions are largely driven by positive and negative effects observed for students at 2-year institutions, and we discuss several hypotheses that may explain these findings.
Mechanical characterization of an innovative dental implant system.

PURPOSE The research presented is aimed at the characterization of the mechanical resistance of an innovative system of an abutment-fixture connection in dental implants. This innovative connection system is composed of a triangular prismatic connection designed to improve the anti-rotational properties of the implant, and to seal any gap between the abutment and the fixture. METHODS The mechanical performances of the dental implant system were investigated by means of static mechanical strength tests, which allowed the identification of the bending, torque and compression resistance of the system, and fatigue testing, according to the practice standard - ISO 14801. Surface finishing was also analyzed by scanning electron microscopy (SEM) observations and laser profilometry tests. RESULTS The analyzed implant exhibited good mechanical characteristics, both in static and in fatigue tests. Moreover, the gap between the fixture and the abutment detected by SEM analyses was restricted, both before and after fatigue tests, being approximately 4 mum in the worst case observed: this is representative of optimal sealing against fluid infiltration. CONCLUSIONS The modification of traditional dental implants with the introduction of a triangular prismatic connection system not only allowed the implant rotational stability and sealing performances to increase, but also conferred optimal mechanical resistance to the implant.
Heat stress decreases testicular germ cell proliferation and increases apoptosis in short term: an immunohistochemical and ultrastructural study

Scrotal hyperthermia has been known as a cause of male infertility but the exact mechanism leading to impaired spermatogenesis is unknown. This work was aimed to investigate the role of scrotal hyperthermia on cell proliferation and apoptosis in testes. The rats were randomly allotted into one of the four experimental groups: A (control), B (1 day after scrotal hyperthermia), C (14 days after scrotal hyperthermia), and D (35 days after scrotal hyperthermia); each group comprised 7 animals. Scrotal hyperthermia was carried out in a thermostatically controlled water bath at 43°C for 30 min once daily for 6 consecutive days. Control rats were treated in the same way, except the testes were immersed in a water bath maintained at 22°C. Hyperthermia-exposed rats were killed under 50 mg/kg ketamine anaesthesia and tissue samples were obtained for biochemical and histopathological investigations. Hyperthermia treatment significantly decreased the testicular antioxidant system, including decreases in the glutathione level, superoxide dismutase, and glutathione peroxidase activities. Moreover, exposure to hyperthermia resulted in lipid peroxidation increase in testes. Our data indicate a significant reduction in the expression of proliferating cell nuclear antigen and an enhancement in the activity of terminal deoxynucleotidyl transferase dUTP nick end labelling after scrotal hyperthermia. In scrotal hyperthermia, the mitochondrial degeneration, dilatation of smooth endoplasmic reticulum, and enlarged intercellular spaces were observed in both Sertoli and spermatid cells. Scrotal hyperthermia is one of the major factors that impair spermatogenesis in testis. This heat stress is shown to be closely associated with oxidative stress, followed by apoptosis of germ cells.
Fast Intra Mode Decision in High Efficiency Video Coding

In this paper a coding unit early termination algorithm resulting in a fast intra prediction is proposed that terminates complete full search prediction for the coding unit. This is followed by a prediction unit mode decision to find the optimal modes HEVC encoder 35 prediction modes. This includes a two-step process: firstly calculating the Sum of Absolute Differences (SAD) of all the modes by down sampling method and secondly applying a three-step search algorithm to remove unnecessary modes. This is followed by early RDOQ (Rate Distortion Optimization Quantization) termination algorithm to further reduce the encoding time. Experimental results based on several video test sequences for 30 frames from each test sequence show for HEVC a decrease of about 35%-48% in encoding, with negligible degradation in peak signal to noise ratio (PSNR). Metrics such as BD-bitrate (Bjontegaard Delta bitrate), BD-PSNR (Bjontegaard Delta Peak Signal to Noise Ratio) and RD plots (Rate Distortion) are also used.
Epilepsy and neuropsychiatric comorbidities

Epilepsy is a common neurological condition with wide-ranging neuropsychiatric manifestations. The relationship between epilepsy and psychiatry has been recognised for centuries. However, the wide range of neuropsychiatric comorbidities and their extent is only now beginning to be appreciated. The impact of these comorbidities on patients’ help-seeking behaviour, seizure control and quality of life suggests that early detection and treatment are of paramount importance. Clinical issues in relation to accurate recognition and appropriate management of neuropsychiatric conditions in epilepsy are discussed.
New challenges in viral hepatitis

Over the past few decades there has been remarkable progress in viral hepatitis. Beginning with discovery of the viral agents, we now have reliable methods to diagnose and monitor all hepatitis virus infections, as well significant advances in treatment and prevention. Nonetheless, important challenges remain. This supplement to Gut looks forward to the next generation of challenges in the field of viral hepatitis, and this introductory article highlights several key issues.
Reverse Transcriptase and Cellular Factors: Regulators of HIV-1 Reverse Transcription

There is ample evidence that synthesis of HIV-1 proviral DNA from the viral RNA genome during reverse transcription requires host factors. However, only a few cellular proteins have been described in detail that affect reverse transcription and interact with reverse transcriptase (RT). HIV-1 integrase is an RT binding protein and a number of IN-binding proteins including INI1, components of the Sin3a complex, and Gemin2 affect reverse transcription. In addition, recent studies implicate the cellular proteins HuR, AKAP149, and DNA topoisomerase I in reverse transcription through an interaction with RT. In this review we will consider interactions of reverse transcription complex with viral and cellular factors and how they affect the reverse transcription process.
Multiple haptic targets for motion-impaired computer users

Although a number of studies have reported that force feedback gravity wells can improve performance in "point-and-click" tasks, there have been few studies addressing issues surrounding the use of gravity wells for multiple on-screen targets. This paper investigates the performance of users, both with and without motion-impairments, in a "point-and-click" task when an undesired haptic distractor is present. The importance of distractor location is studied explicitly. Results showed that gravity wells can still improve times and error rates, even on occasions when the cursor is pulled into a distractor. The greatest improvement is seen for the most impaired users. In addition to traditional measures such as time and errors, performance is studied in terms of measures of cursor movement along a path. Two cursor measures, angular distribution and temporal components, are proposed and their ability to explain performance differences is explored.
A comparison of X-ray and proton beam low energy secondary electron track structures using the low energy models of Geant4

Abstract Purpose: Lethal cell damage by ionising radiation is generally initiated by the formation of complex strand breaks, resulting from ionisation clusters in the DNA molecule. A better understanding of the effect of the distribution of ionisation clusters within the cell and particularly in regard to DNA segments could be beneficial to radiation therapy treatment planning. Low energy X-rays generate an abundance of low energy electrons similar to that associated with MeV protons. The study and comparison of the track structure of photon and proton beams could permit the substitution of photon microbeams for single cell ion irradiations at proton facilities used to predict the relative biological effectiveness (RBE) of charged particle fields. Materials and methods: The track structure of X-ray photons is compared with proton pencil beams in voxels of approximate DNA strand size (2 × 2 × 5 nm). The Very Low Energy extension models of the Monte Carlo simulation toolkit GEometry ANd Tracking 4 (Geant4) is used. Simulations were performed in a water phantom for an X-ray and proton beam of energies 100 keV and 20 MeV, respectively. Results: The track structure of the photon and proton beams are evaluated using the ionisation cluster size distribution as well as the radial dose deposition of the beam. Conclusions: A comparative analysis of the ionisation cluster distribution and radial dose deposition obtained is presented, which suggest that low energy X-rays could produce similar ionisation cluster distributions to MeV protons on the DNA scale of size at depths greater than ∼10 μm and at distances greater than ∼1 μm from the beam centre. Here the ionisation cluster size for each beam is less than ∼100. The radial dose deposition is also approximately equal at large depths and at distances greater than 10 μm from the beam centre.
The threshold join algorithm for top-k queries in distributed sensor networks

In this paper we present the Threshold Join Algorithm (TJA), which is an efficient TOP-k query processing algorithm for distributed sensor networks. The objective of a top-k query is to find the k highest ranked answers to a user defined similarity function. The evaluation of such a query in a sensor network environment is associated with the transfer of data over an extremely expensive communication medium. TJA uses a non-uniform threshold on the queried attribute in order to minimize the number of tuples that have to be transferred towards the querying node. Additionally, TJA resolves queries in the network rather than in a centralized fashion, which minimizes even more the consumption of bandwidth and delay. Our preliminary experimental results, using our trace driven simulator, show that TJA is both practical and efficient.
Distributed Projection-Based Algorithms for Source Localization in Wireless Sensor Networks

In this paper, we investigate source localization for wireless sensor networks based on received signal strength. We first formulate the localization problem as the intersection computation of a group of sensing rings, and then convert this non-convex problem into two weighted convex optimization problems. We next propose a unified distributed alternating projection algorithm to solve the resulting weighted optimization problems, where sensor nodes can communicate only locally with their neighbors over a time-varying jointly-connected topology. We also show that sensor nodes' estimates can achieve consensus on a possible minimizer. Both theoretical analysis and some comparative simulations reveal that the proposed approach has good estimation performance in both the consistent and inconsistent cases.
A different approach to high performance computing

A common approach to enhance the performance of processors is to increase the number of function units which operate concurrently. We observe this development in all recent superscalar and VLIW (very-long instruction word) processors. VLIWs are easier extensible to high performance ranges because they lack much of the superscalar hardware required for dependence checking and hardware resource allocation; instead they rely on a compiler to perform these tasks. In this paper, we proceed along this line and go one step further in replacing hardware by software complexity: a new architecture is proposed which requires the scheduling and allocation of transports at compile-time, instead of performing this at run-time. This reduces hardware complexity and creates several new compile-time optimizations. The paper illustrates the compilation steps required, explains the concept and characteristics of the proposed architecture, and shows several measurements which confirm our belief that, especially for high-performance embedded applications, this architecture is very attractive.
The American Family in Black and White: A Post-Racial Strategy for Improving Skills to Promote Equality

In contemporary America, racial gaps in achievement are primarily due to gaps in skills. Skill gaps emerge early before children enter school. Families are major producers of those skills. Inequality in performance in school is strongly linked to inequality in family environments. Schools do little to reduce or enlarge the gaps in skills that are present when children enter school. Parenting matters, and the true measure of child advantage and disadvantage is the quality of parenting received. A growing fraction of American children across all race and ethnic groups is being raised in dysfunctional families. Investment in the early lives of children in disadvantaged families will help close achievement gaps. America currently relies too much on schools and adolescent remediation strategies to solve problems that start in the preschool years. Prevention is likely to be more cost-effective than remediation. Voluntary, culturally sensitive support for parenting is a politically and economically palatable strategy that addresses problems common to all racial and ethnic groups.
The Cognitive Neuroscience of Music

Music perception and performance rely heavily on temporal processing: for instance, each event must be situated in time in relation to surrounding events, and events must be grouped together in order to overcome memory constraints. The temporal structure of music varies considerably from one culture to another, and so it has often been supposed that the specific implementation of perceptual and cognitive temporal processes will differ as a function of an individual’s cultural exposure and experience. In this paper we examine the alternative position that some temporal processes may be universal, in the sense that they function in a similar manner irrespective of an individual’s cultural exposure and experience. We first review rhythm perception and production studies carried out with adult musicians, adult nonmusicians, children, and infants in order to identify temporal processes that appear to function in a similar fashion irrespective of age, acculturation, and musical training. This review leads to the identification of five temporal processes that we submit as candidates for the status of ‘temporal universals’. For each process, we select the simplest and most representative experimental paradigm that has been used to date. This leads to a research proposal for future intercultural studies that could test the universal nature of these processes.
Effects of glucagon on hepatic glycogen and smooth endoplasmic reticulum.

The action of glucagon on hepatic glycogen and smooth endoplasmic reticulum (SER) was studied in samples of liver taken sequentially from anesthetized rats. The physiological state of each animal was assessed by continuously monitoring aortic blood pressure and blood lactatepyruvate ratios. High hepatic glycogen levels were established by using 10--12 hr fasted control-fed rats infused continuously with glucose. In rats receiving glucose only, hepatic glycogen levels remained above 5.0% during the 4-hr period of glucose administration. Centrilobular hepatocytes displayed an abundance of glycogen which often appeared dispersed with elements of SER between the glycogen particles. Periportal cells had dense clumps of glycogen with few vesicles of SER restricted to the periphery of the glycogen masses. The addition of glucagon to the glucose infusate caused a marked stimulation of glycogenolysis. In these rats, the hepatic glycogen level (X +/- SE) was 6.74 +/- . 15% 1 hr after glucose and declined after initiation of glucagon infusion as follows: 5.86 +/- . 29% (15 min), 4.89 +/- . 26% (1 hr), 2.16 +/- . 40% (2 hr), and 1.66 +/- . 29% (3 hr). The fine structure of hepatocytes showed a dramatic response to the administration of glucagon. The glycogen regions of the cells were noticeably decreased in size and number of glycogen granules 3 hr after initiation of glucagon infusion, and SER was abundant in both periportal and centrilobular hepatocytes. The interpretation offered is that glucagon induces the formation of new SER membranes which participate in glycogen breakdown and/or glucose release from hepatocytes.