Miracle-dz/UniFAR-FTUs huggingface dataset:
The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

Viral defense and embryo implantation mechanisms have been shaped by contributions from Neandertal and Denisovan genes. Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.
Demonstration of a functional quantum-dot cellular automata cell

We report an experimental demonstration of a functional cell for quantum-dot cellular automata (QCA), a transistorless approach to implement logic functions. The four-dot QCA cell is defined by a pair of series-connected, capacitively coupled input and output double dots. We demonstrate that, at low temperature, an electron switch in the input double dot induces an opposite electron switch in the output double dot, resulting in a complete polarization change of the QCA cell. Switching is verified by electrometer signals which are coupled to the output double dot. Experimental results suggest that electron motion in the coupled double dots is strongly correlated and can support high operating frequencies. Agreement between theoretical predictions and experimentally measured values of the dot potentials is excellent.
Efficacy of an evidence-based cognitive stimulation therapy programme for people with dementia

Background A recent Cochrane review of reality orientation therapy identified the need for large, well-designed, multi-centre trials. Aims To test the hypothesis that cognitive stimulation therapy (CST) for older people with dementia would benefit cognition and quality of life. Method A single-blind, multi-centre, randomised controlled trial recruited 201 older people with dementia. The main outcome measures were change in cognitive function and quality of life. An intention-to-treat analysis used analysis of covariance to control for potential variability in baseline measures. Results One hundred and fifteen people were randomised within centres to the intervention group and 86 to the control group. At follow-up the intervention group had significantly improved relative to the control group on the Mini-Mental State Examination (P=0.044), the Alzheimer's Disease Assessment Scale – Cognition (ADAS–Cog) (P=0.014) and Quality of Life – Alzheimer's Disease scales (P=0.028). Using criteria of 4 points or more improvement on the ADAS–Cog the number needed to treat was 6 for the intervention group. Conclusion The results compare favourably with trials of drugs for dementia. CST groups may have worthwhile benefits for many people with dementia.
Cochlear Implantation, Synaptic Plasticity and Auditory Function

The ability to hear, our perception of sound, is fundamental to how we perceive our external environment and interact with others using spoken language. Sound also plays a critical role in the normal development of the auditory system. In this review, we will discuss sound, hearing, and the role of hearing in brain development. We will examine the effect of deafness and the impact of cochlear implants on neuronal plasticity and auditory function.
Thin Film Filter Based Components for Optical Add/Drop

Optical thin film interference filters are well suited for the demanding application of optical add/drop. They are passive in nature with low insertion loss and possess a square filter function. They are easily packaged into robust, environmentally stable fiber pigtailed packages. This paper discusses a number of applications and issues surrounding the use of thin film optical filters for optical add/drop. It includes a discussion of switched or reconfigurable optical add/drops, hybridization of switches and filters, and the effect of concatenation of a series of identical filters.
H∞ gain scheduling for discrete-time systems with control delays and time-varying parameters: a BMI approach

In this paper, the problem of gain scheduling for time-varying systems with time delays is investigated. By using a memory at the feedback loop, a discrete gain scheduled controller which minimizes an upper bound to the ,Hscrinfin performance of the closed loop system is determined. The design conditions, expressed in terms of bilinear matrix inequalities, are obtained from the Finsler's Lemma combined with the Lyapunov theory. The extra variables introduced by the Finsler's Lemma represent an alternative way in the search of better system behavior. The time-varying uncertainties are modeled using polytopic domains. The controller is obtained by the solution of an optimization problem formulated only in terms of the vertices of the polytope. No grids in the parametric space are used. Numerical examples illustrate the efficiency of the proposed approach.
Structure and Antioxidant Activities of Proanthocyanidins from Elephant Apple (Dillenia indica Linn.).

UNLABELLED Proanthocyanidins were isolated and purified from fruits of elephant apple (Dillenia indica Linn.) and their structural and bioactive properties were examined. Bate-Smith alcoholysis, FTIR, and (13) C NMR spectra revealed that elephant apple proanthocyanidins (EAPs) contained a dominant amount of B-type procyanidins (PC) with a minor amount of B-type prodelphinidins (PD) but no A-type interflavan linkage. (13) C NMR spectrum indicated that the cis isomer was dominant in EAPs. The electron spray ionization and matrix-assisted laser desorption ionization time of flight mass spectra of EAPs showed the clear ion peaks corresponding to B-type PC dimer to B-type PD with degree of polymerization of 11. EAPs had strong antioxidant activity, which was evidenced by the high oxygen radical scavenging capacity at 1.06 × 10(4) μmol TE/g and ferric reducing antioxidant power of 2320 μmol Fe(II)/g. The results suggest that EAPs could be extracted to be used as promising functional food materials. PRACTICAL APPLICATION In this study, the elephant apple proanthocyanidins (EAPs) with a yield of 0.23% were identified for the first time as dominant B-type poly(catechin/epicatechin) but no A-type interflavan linkage. EAPs had higher ORAC and FRAP values compared to commercial grape seed proanthocyanidins, suggesting that EAPs may be used as promising functional food materials.
Modelling contrasting responses of wetland productivity to changes in water table depth

Abstract. Responses of wetland productivity to changes in water table depth (WTD) are controlled by complex interactions among several soil and plant processes, and hence are site-specific rather than general in nature. Hydrological controls on wetland productivity were studied by representing these interactions in connected hummock and hollow sites in the ecosystem model ecosys, and by testing CO2 and energy fluxes from the model with those measured by eddy covariance (EC) during years with contrasting WTD in a shrub fen at Lost Creek, WI. Modelled interactions among coupled processes for O2 transfer, O2 uptake, C oxidation, N mineralization, N uptake and C fixation by diverse microbial, root and mycorrhizal populations enabled the model to simulate complex responses of CO2 exchange to changes in WTD that depended on the WTD at which change was occurring. At the site scale, greater WTD caused the model to simulate greater CO2 influxes and effluxes over hummocks vs. hollows, as has been found at field sites. At the landscape scale, greater WTD caused the model to simulate greater diurnal CO2 influxes and effluxes under cooler weather when water tables were shallow, but also smaller diurnal CO2 influxes and effluxes under warmer weather when water tables were deeper, as was also apparent in the EC flux measurements. At an annual time scale, these diurnal responses to WTD in the model caused lower net primary productivity (NPP) and heterotrophic respiration (Rh), but higher net ecosystem productivity (NEP = NPP − Rh), to be simulated in a cooler year with a shallower water table than in a warmer year with a deeper one. This difference in NEP was consistent with those estimated from gap-filled EC fluxes in years with different water tables at Lost Creek and at similar boreal fens elsewhere. In sensitivity tests of the model, annual NEP declined with increasing WTD in a year with a shallow water table, but rose in a year with a deeper one. The model thus provided an integrated set of hypotheses for explaining site-specific and sometimes contrasting responses of wetland productivity to changes in WTD as found in different field experiments.
Partitioning Sparse Rectangular Matrices for Parallel Processing ?

We are interested in partitioning sparse rectangular matrices for parallel processing. The partitioning problem has been well-studied in the square symmetric case, but the rectangular problem has received very little attention. We will formalize the rectangular matrix partitioning problem and discuss several methods for solving it. We will extend the spectral partitioning method for symmetric matrices to the rectangular case and compare this method to three new methods | the alternating partitioning method and two hybrid methods. The hybrid methods will be shown to be best.
Color and Psychological Functioning

Color is a ubiquitous perceptual experience, yet little scientific information about the influence of color on affect, cognition, and behavior is available. Accordingly, we have developed a general model of color and psychological functioning, which we present in this article. We also describe a hypothesis derived from this model regarding the influence of red in achievement contexts. In addition, we report a series of experiments demonstrating that a brief glimpse of red evokes avoidance motivation and undermines intellectual performance, and that it has these effects without conscious awareness or intention. We close with thoughts on the need for rigorous scientific work on color psychology.
Titanium foam‐bioactive nanofiber hybrids for bone regeneration

We have reported previously a method to introduce bioactive nanofiber networks through self‐assembly into the pores of titanium alloy foams for bone repair. In this study we evaluate the in vitro colonization by mouse pre‐osteoblastic cells of these metal–peptide amphiphile hybrids containing phosphoserine residues and the RGDS epitope. The aim was to determine the effect of varying the RGDS epitope concentration within a given range, and confirm the ability for cells to infiltrate and survive within the nanofiber‐filled interconnected porosity of the hybrid material. We performed proliferation (DNA content) and differentiation assays (alkaline phosphatase and osteopontin expression) as well as SEM and confocal microscopy to evaluate cell colonization of the hybrids. At the RGDS epitope concentrations used in the nanofiber networks, all samples demonstrated significant cell migration into the hybrids, proliferation, and differentiation into osteoblastic lineage. Copyright © 2008 John Wiley & Sons, Ltd.
ON SELF-ADJOINT OPERATORS IN KREIN SPACES CONSTRUCTED BY CLIFFORD ALGEBRA Cl2

Let \(J\) and \(R\) be anti-commuting fundamental symmetries in a Hilbert space \(\mathfrak{H}\). The operators \(J\) and \(R\) can be interpreted as basis (generating) elements of the complex Clifford algebra \(Cl_2(J,R):=\text{span}\{I,J,R,iJR\}\). An arbitrary non-trivial fundamental symmetry from \(Cl_2(J,R)\) is determined by the formula \(J_{\vec{\alpha}}=\alpha_1 J +\alpha_2 R+\alpha_3 iJR\), where \(\vec{\alpha} \in \mathbb{S}^2\). Let \(S\) be a symmetric operator that commutes with \(Cl_2(J,R)\). The purpose of this paper is to study the sets \(\Sigma_{J_{\vec{\alpha}}}\) (\(\forall \vec{\alpha} \in \mathbb{S}^2\)) of self-adjoint extensions of \(S\) in Krein spaces generated by fundamental symmetries \(J_{\vec{\alpha}}\) (\(J_{\vec{\alpha}}\)-self-adjoint extensions). We show that the sets \(\Sigma_{J_{\vec{\alpha}}}\) and \(\Sigma_{J_{\vec{\beta}}}\) are unitarily equivalent for different \(\vec{\alpha}, \vec{\beta} \in \mathbb{S}^2\) and describe in detail the structure of operators \(A \in \Sigma_{J_{\vec{\alpha}}}\) with empty resolvent set.
Management of anticancer treatment in patients under chronic dialysis: results of the multicentric CANDY (CANcer and DialYsis) study.

BACKGROUND One million people worldwide benefit from chronic dialysis, with an increased rate in Western countries of 5% yearly. Owing to increased incidence of cancer in dialyzed patients, the management of these patients is challenging for oncologists/nephrologists. PATIENTS AND METHODS The CANcer and DialYsis (CANDY) retrospective multicenter study included patients under chronic dialysis who subsequently had a cancer (T0). Patients were followed up for 2 years after T0. Prescriptions of anticancer drugs were studied with regard to their renal dosage adjustment/dialysability. RESULTS A total of 178 patients from 12 institutions were included. The mean time between initiation of dialysis and T0 was 30.8 months. Fifty patients had received anticancer drug treatment. Among them, 72% and 82% received at least one drug needing dosage and one drug to be administered after dialysis sessions, respectively. Chemotherapy was omitted or prematurely stopped in many cases where systemic treatment was indicated or was often not adequately prescribed. CONCLUSIONS Survival in dialysis patients with incident cancer was poor. It is crucial to consider anticancer drug treatment in these patients as for non-dialysis patients and to use current available specific drug management recommendations in order to (i) adjust the dose and (ii) avoid premature elimination of the drug during dialysis sessions.
The Role of Multimerization During Non-Homologous End Joining

In order to sustain life, cells must protect their genetic information from the constant threat posed by mutagenic agents such as ultraviolet light, irradiation or reactive oxy‐ gen species, as well as from mistakes introduced during the replication of their ge‐ nomes [1]. To deal with this problem, natural selection has favored a system that repairs the damage caused by these DNA lesions while allowing the highly infrequent but steady production of mutations that constitute the source for adaptive changes dur‐ ing evolution. To repair damaged DNA, cells have developed a myriad of highly speci‐ alized pathways that recognize and repair specific types of injuries produced by specific types of mutagenic events [2, 3]. For instance, while base excision repair detects and re‐ pairs chemically damaged nucleotide bases typically produced by oxygen radicals or al‐ kylating agents, nucleotide excision repair is responsible for the removal of thymine dimers caused by ultraviolet light exposure. Additionally, the mismatch repair pathway specializes in fixing errors introduced during DNA replication. More globally, these pathways are part of the DNA damage response (DDR), a signal transduction cascade coordinated by the ATM/ATR kinases in mammalian cells that halts cell cycle progres‐ sion while DNA is being repaired, and it can trigger apoptosis when the damage is deemed non-repairable [4]. The importance of these pathways is underlined by their high conservation, both in prokaryotes and eukaryotes, and it is emphasized by the role that they play in disease when impaired. Malfunctioning DNA repair pathways are as‐ sociated with several disorders such as Xeroderma pigmentosum or Nijmegen syn‐ drome as well as with increased cancer risk, as they boost the formation of spontaneous mutations that can lead to tumorigenesis [5].
Targeted Over-Expression of Glutamate Transporter 1 (GLT-1) Reduces Ischemic Brain Injury in a Rat Model of Stroke

Following the onset of an ischemic brain injury, the excitatory neurotransmitter glutamate is released. The excitotoxic effects of glutamate are a major contributor to the pathogenesis of a stroke. The aim of this study was to examine if overexpression of a glutamate transporter (GLT-1) reduces ischemic brain injury in a rat model of stroke. We generated an adeno-associated viral (AAV) vector expressing the rat GLT-1 cDNA (AAV-GLT1). Functional expression of AAV-GLT1 was confirmed by increased glutamate clearance rate in non-stroke rat brain as measured by in vivo amperometry. AAV-GLT1 was injected into future cortical region of infarction 3 weeks prior to 60 min middle cerebral artery occlusion (MCAo). Tissue damage was assessed at one and two days after MCAo using TUNEL and TTC staining, respectively. Behavioral testing was performed at 2, 8 and 14 days post-stroke. Animals receiving AAV-GLT1, compared to AAV-GFP, showed significant decreases in the duration and magnitude of extracellular glutamate, measured by microdialysis, during the 60 minute MCAo. A significant reduction in brain infarction and DNA fragmentation was observed in the region of AAV-GLT1 injection. Animals that received AAV-GLT1 showed significant improvement in behavioral recovery following stroke compared to the AAV-GFP group. We demonstrate that focal overexpression of the glutamate transporter, GLT-1, significantly reduces ischemia-induced glutamate overflow, decreases cell death and improves behavioral recovery. These data further support the role of glutamate in the pathogenesis of ischemic damage in brain and demonstrate that targeted gene delivery to decrease the ischemia-induced glutamate overflow reduces the cellular and behavioral deficits caused by stroke.
Vision-based 3d human motion analysis for fall detection and bed-exiting

Fall is one of the most dangerous and costly accidents that threaten health of elderly people, and a large portion of falls occurs when a patient is trying to exit a bed. This thesis proposes two vision-based approaches for general fall detection and bed-exiting detection for elderly people, respectively. The Kinect sensor is chosen as the major monitoring device. The first approach exploits the Kinect sensor with its Windows SDK to detect fall activities. The recorded spatial coordinates of the human body joints from Kinect’s 3D skeletal view are processed to extract posture features. Then the principle component analysis and k-means clustering algorithms are applied for dimensionality reduction, vector quantization and feature translation. HMMs are well known for their application in temporal pattern recognition, thus they are chosen for this project to classify human motion which is a temporal sequence of postures. HMMs are trained by the labelled extracted features to model and discriminate four fall motion classes and three non-fall classes. The second approach utilizes segmented motion history image (MHI) sequences to extract spatiotemporal features of a moving human body. Eight Hu image moments are calculated to translate the spatiotemporal features of each frame into vectors to describe video frames. The k-means clustering and HMM modelling are utilized for vector quantization and classification between bed-exiting activities and
Markov Modeling of Component Fault Growth Over A Derived Domain of Feasible Output Control Effort Modifications

This paper introduces a novel Markov process formulation of stochastic fault growth modeling, in order to facilitate the development and analysis of prognostics-based control adaptation. A metric representing the relative deviation between the nominal output of a system and the net output that is actually enacted by an implemented prognostics-based control routine, will be used to define the action space of the formulated Markov process. The state space of the Markov process will be defined in terms of an abstracted metric representing the relative health remaining in each of the system’s components. The proposed formulation of component fault dynamics will conveniently relate feasible system output performance modifications to predictions of future component health deterioration.
Screening of colorectal cancer: present and future

ABSTRACT Introduction: Colorectal cancer (CRC) is the third most common cancer in males and second in females, and the fourth most common cause of cancer death worldwide. Currently, about 60–70% of diagnosed cases in symptomatic patients are detected at an advanced stage of disease. Earlier stage detection through the use of screening strategies would allow for better outcomes in terms of reducing the disease burden. Areas covered: The aim of this paper is to review the current published evidence from literature which assesses the performance and effectiveness of different screening tests for the early detection of CRC. Expert commentary: Adequate screening strategies can reduce CRC incidence and mortality. In the last few decades, several tests have been proposed for CRC screening. To date, there is still insufficient evidence to identify which approach is definitively superior, and no screening strategy for CRC can therefore be defined as universally ideal. The best strategy would be the one that can be economically viable and to which the patient can adhere best to over time. The latest guidelines suggest colonoscopy every 10 years or annual fecal immuno-chemical test (FIT) for people with normal risk, while for individuals with high risk or hereditary syndromes specific recommendations are provided.
Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays

Copy Number Variants (CNV) and other submicroscopic structural changes are now recognised to be widespread across the human genome. We show that SNP data generated for association study can be utilised for the identification of deletion CNVs. During analysis of data for an SNP association study for Specific Language Impairment (SLI) a deletion was identified. SLI adversely affects the language development of children in the absence of any obvious cause. Previous studies have found linkage to a region on chromosome 16. The deletion was located in a known fragile site FRA16D in intron 5–6 of the WWOX gene (also known as FOR). Changes in the FRA16D site have been previously linked to cancer and are often characterised in cell lines. A long-range PCR assay was used to confirm the existence of the deletion. We also show the breakpoint identification and large-scale characterisation of this CNV in a normal human sample set.
RNAi-mediated knockdown of E2F2 inhibits tumorigenicity of human glioblastoma cells

In a previous genome-wide expression profiling study, we identified E2F2 as a hyperexpressed gene in stem-like cells of distinct glioblastoma multiforme (GBM) specimens. Since the encoded E2F2 transcription factor has been implicated in both tumor suppression and tumor development, we conducted a functional study to investigate the pertinence of E2F2 to human gliomagenesis. E2F2 expression was knocked down by transfecting U87MG cells with plasmids carrying a specific silencing shRNA. Upon E2F2 silencing, in vitro cell proliferation was significantly reduced, as indicated by a time-course analysis of viable tumor cells. Anchorage-independent cell growth was also significantly inhibited after E2F2 silencing, based on cell colony formation in soft agar. Subcutaneous and orthotopic xenograft models of GBM in nude mice also indicated inhibition of tumor development in vivo, following E2F2 silencing. As expression of the E2F2 gene is associated with glioblastoma stem cells and is involved in the transformation of human astrocytes, the present findings suggest that E2F2 is involved in gliomagenesis and could be explored as a potential therapeutic target in malignant gliomas.