Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuropsychological Performance in Persons With Chronic Fatigue Syndrome: Results From a Population-Based Study

Objective: To examine the neuropsychological function characterized in subjects with chronic fatigue syndrome (CFS) at the same time controlling for relevant confounding factors. CFS is associated with symptoms of neuropsychological dysfunction. Objective measures of neuropsychological performance have yielded inconsistent results possibly due to sample selection bias, diagnostic heterogeneity, comorbid psychiatric disorders, and medication usage. Method: CFS subjects (n = 58) and well controls (n = 104) from a population-based sample were evaluated, using standardized symptom severity criteria. Subjects who had major psychiatric disorders or took medications known to influence cognition were excluded. Neuropsychological function was measured using the Cambridge Neuropsychological Test Automated Battery (CANTAB). Results: Compared with controls, CFS subjects exhibited significant decreases in motor speed as measured in the simple and five-choice movement segments of the CANTAB reaction time task. CFS subjects also exhibited alterations in working memory as manifested by a less efficient search strategy on the spatial working memory task, fewer % correct responses on the spatial recognition task, and prolonged latency to a correct response on the pattern recognition task. A significantly higher percentage of CFS subjects versus controls exhibited evidence of neuropsychological impairment (defined by performance 1 standard deviation below the CANTAB normative mean) in tasks of motor speed and spatial working memory. Impairment in CFS subjects versus control subjects ranged from 20% versus 4.8% in five-choice movement time (p = .002) to 27.8% versus 10.6% in search strategy on the spatial working memory task (p = .006). Conclusions: These results confirm and quantify alterations in motor speed and working memory in CFS subjects independent of comorbid psychiatric disease and medication usage. CFS = chronic fatigue syndrome; MFI = Multidimensional Fatigue Inventory; SCID = Structured Clinical Interview for DSM-IV; SDS = Zung Self-Rating Depression Scale; WRAT-3 = Wide Range Achievement Test 3; CANTAB = Cambridge Neuropsychological Test Automated Battery; RTI = reaction time; RVIP = rapid visual information processing; SWM = spatial working memory; PRM = pattern recognition memory; SRM = spatial recognition memory; EDS = extra-dimensional shift; ANCOVA = analysis of covariance; MANCOVA = multivariate analysis of covariance.
Models of receptive-field dynamics in visual cortex

The position, size, and shape of the receptive field (RF) of some cortical neurons change dynamically, in response to artificial scotoma conditioning (Pettet & Gilbert, 1992) and to retinal lesions (Chino et al., 1992; Darian-Smith & Gilbert, 1995) in adult animals. The RF dynamics are of interest because they show how visual systems may adaptively overcome damage (from lesions, scotomas, or other failures), may enhance processing efficiency by altering RF coverage in response to visual demand, and may perform perceptual learning. This paper presents an afferent excitatory synaptic plasticity rule and a lateral inhibitory synaptic plasticity rule—the EXIN rules (Marshall, 1995)—to model persistent RF changes after artificial scotoma conditioning and retinal lesions. The EXIN model is compared to the LISSOM model (Sirosh et al., 1996) and to a neuronal adaptation model (Xing & Gerstein, 1994). The rules within each model are isolated and are analyzed independently, to elucidate their roles in adult cortical RF dynamics. Based on computer simulations, the EXIN lateral inhibitory synaptic plasticity rule and the LISSOM lateral excitatory synaptic plasticity rule produced the best fit with current neurophysiological data on visual cortical plasticity in adult animals (Chino et al., 1992; Pettet & Gilbert, 1992; Darian-Smith & Gilbert, 1995) including (1) the retinal position and shape of the expanding RFs; (2) the corticotopic direction in which responsiveness returns to the silenced cortex; (3) the direction of RF shifts; (4) the amount of change in response to blank stimuli; and (5) the lack of dynamic RF changes during conditioning with a retinal lesion in one eye and the unlesioned eye kept open, in adult animals. The effects of the LISSOM lateral inhibitory synaptic plasticity rule during artificial scotoma conditioning are in conflict with those of the other two LISSOM synaptic plasticity rules. A novel “complementary scotoma” conditioning experiment, in which stimulation of two complementary regions of visual space alternates repeatedly, is proposed to differentiate the predictions of the EXIN and LISSOM rules.
Combining convolutional and recurrent neural networks for Alzheimer's disease diagnosis using PET images

Alzheimer's disease (AD) is a progressive and irreversible brain degenerative disorder which often happens in people aged more than 65 years old. Accurate and early diagnosis of AD is vital for the patient care and development of future treatment. Positrons Emission Tomography (PET) is a functional molecular imaging modality, which proves to be a powerful tool to help understand the brain changes related to AD. Most existing methods extract the handcraft features from images, and then train a classifier to distinguish AD from other groups. The success of these computer-aided diagnosis methods highly depends on the image preprocessing, including rigid registration and segmentation. Motivated by the success of deep learning in image classification, this paper proposes a new classification framework based on combination of 2D convolutional neural networks (CNN) and recurrent neural networks (RNN), which learns the features of 3D PET images by decomposing the 3D image into a sequence of 2D slices. In this framework, the hierarchical 2D CNNs are built to capture the intra-slice features while the gated recurrent unit (GRU) of RNN is used to extract the inter-slice features for final classification. No rigid image registration and segmentation are required for PET images. Our method is evaluated on the baseline PET images from 339 subjects including 93 AD patients, 146 mild cognitive impairments (MCI) and 100 normal controls (NC) from Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Experimental results show that the proposed method achieves an AUC of 95.28% for classification of AD vs. NC and 83.90% for classification of MCI vs. NC, respectively, demonstrating the promising classification performance.
The accuracy of HIV rapid testing in integrated bio-behavioral surveys of men who have sex with men across 5 Provinces in South Africa

Abstract We describe the accuracy of serial rapid HIV testing among men who have sex with men (MSM) in South Africa and discuss the implications for HIV testing and prevention. This was a cross-sectional survey conducted at five stand-alone facilities from five provinces. Demographic, behavioral, and clinical data were collected. Dried blood spots were obtained for HIV-related testing. Participants were offered rapid HIV testing using 2 rapid diagnostic tests (RDTs) in series. In the laboratory, reference HIV testing was conducted using a third-generation enzyme immunoassay (EIA) and a fourth-generation EIA as confirmatory. Accuracy, sensitivity, specificity, positive predictive value, negative predictive value, false-positive, and false-negative rates were determined. Between August 2015 and July 2016, 2503 participants were enrolled. Of these, 2343 were tested by RDT on site with a further 2137 (91.2%) having definitive results on both RDT and EIA. Sensitivity, specificity, positive predictive value, negative predictive value, false-positive rates, and false-negative rates were 92.6% [95% confidence interval (95% CI) 89.6–94.8], 99.4% (95% CI 98.9–99.7), 97.4% (95% CI 95.2–98.6), 98.3% (95% CI 97.6–98.8), 0.6% (95% CI 0.3–1.1), and 7.4% (95% CI 5.2–10.4), respectively. False negatives were similar to true positives with respect to virological profiles. Overall accuracy of the RDT algorithm was high, but sensitivity was lower than expected. Post-HIV test counseling should include discussions of possible false-negative results and the need for retesting among HIV negatives.
Separation of organic and inorganic arsenic species by capillary electrophoresis using direct spectrophotometric detection

Capillary electrophoresis (CE) with UV detection was used for the determination of arsenite, arsenate, monomethylarsonic acid, dimethylarsinic acid, p‐aminophenylarsonic acid, 4‐hydroxy‐3‐nitrobenzenearsonic acid, 4‐nitrophenylarsonic acid, phenylarsonic acid, and phenylarsine oxide. The electrophoretic mobilities of these anionic species were determined in a 20 mM phosphate buffer in a pH range from 4 to 11, which established pH 10 as the optimum for the separation. The target analytes were then separated in a fused‐silica capillary using 20 mM NaHCO3‐Na2CO3 buffer, pH 10, as electrolyte and detected at 192 nm. Both normal‐ and reversed electroosmotic flow (EOF) separation modes were investigated and in the latter case, poly(diallydimethylammonium chloride) (PDDAC), was used for dynamic coating of the capillary and to provide a stable and reproducible reversed EOF (relative standard deviation RSD, 0.39%). The influence of electrolyte pH and composition, applied voltage, as well as EOF reversal protocols upon the method performance criteria were investigated. The optimised method provided limits of detection for the target analytes of 1.62, 6.22, 1.45, 1.83, 0.34, 0.40, 0.40, 0.18, and 0.30 mg/L As, respectively. Linearity was obtained in the range of 0.5–40 mg/L As (for aryl compounds) and from 5–100 mg/L As (for the remaining analytes). Reproducibility of peak areas was in the range of 0.8–5.5% RSD. The method was applied to the determination of four aryl arsenic compounds used as additives in animal feed. Analytes were extracted with 40 mM hydrochloric acid – acetonitrile 4:1 v/v, and then cleaned up by passing through a C18 solid‐phase extraction cartridge before analysis by CE with detection at 200 nm. Recoveries for the four analytes were in the range of 78.8–108.3%.
Cancer and diabetes ‐ a follow‐up study of two populationbased cohorts of diabetic patients

Abstract. Hjalgrim H, Frisch M, Ekbom A, Kyvik KO, Melbye M, Green A (Statens Serum Institut, Copenhagen; Odense University, Odense; Denmark; and University Hospital, Uppsala, Sweden). Cancer and diabetes ‐ a follow‐up study of two population‐ based cohorts of diabetic patients.
Localization of the N terminus of hepatitis B virus capsid protein by peptide-based difference mapping from cryoelectron microscopy.

Recently, cryoelectron microscopy of isolated macromolecular complexes has advanced to resolutions below 10 A, enabling direct visualization of alpha-helical secondary structure. To help correlate such density maps with the amino acid sequences of the component proteins, we advocate peptide-based difference mapping, i. e. , insertion of peptides, approximately 10 residues long, at targeted points in the sequence and visualization of these peptides as bulk labels in cryoelectron microscopy-derived difference maps. As proof of principle, we have appended an extraneous octapeptide at the N terminus of hepatitis B virus capsid protein and determined its location on the capsid surface by difference imaging at 11 A resolution. Hepatitis B virus capsids are icosahedral particles, approximately 300 A in diameter, made up of T-shaped dimers (subunit Mr, 16-21 kDa, depending on construct). The stems of the Ts protrude outward as spikes, whereas the crosspieces pack to form the contiguous shell. The two N termini per dimer reside on either side of the spike-stem, at the level at which it enters the shell. This location is consistent with formation of the known intramolecular disulfide bond between the cysteines at positions 61 and -7 (in the residual propeptide) in the "e-antigen" form of the capsid protein and has implications for why this clinically important antigen remains unassembled in vivo.
Two-step FEM-based Liver-CT registration: improving internal and external accuracy

To know the exact location of the internal structures of the organs, especially the vasculature, is of great importance for the clinicians. This information allows them to know which structures/vessels will be affected by certain therapy and therefore to better treat the patients. However the use of internal structures for registration is often disregarded especially in physical based registration methods. In this paper we propose an algorithm that uses finite element methods to carry out a registration of liver volumes that will not only have accuracy in the boundaries of the organ but also in the interior. Therefore a graph matching algorithm is used to find correspondences between the vessel trees of the two livers to be registered. In addition to this an adaptive volumetric mesh is generated that contains nodes in the locations in which correspondences were found. The displacements derived from those correspondences are the input for the initial deformation of the model. The first deformation brings the internal structures to their final deformed positions and the surfaces close to it. Finally, thin plate splines are used to refine the solution at the boundaries of the organ achieving an improvement in the accuracy of 71%. The algorithm has been evaluated in CT clinical images of the abdomen.
Recent advances in rational gene transfer vector design based on poly(ethylene imine) and its derivatives

The continually increasing wealth of knowledge about the role of genes involved in acquired or hereditary diseases renders the delivery of regulatory genes or nucleic acids into affected cells a potentially promising strategy. Apart from viral vectors, non‐viral gene delivery systems have recently received increasing interest, due to safety concerns associated with insertional mutagenesis of retro‐viral vectors. Especially cationic polymers may be particularly attractive for the delivery of nucleic acids, since they allow a vast synthetic modification of their structure enabling the investigation of structure‐function relationships. Successful clinical application of synthetic polycations for gene delivery will depend primarily on three factors, namely (1) an enhancement of the transfection efficiency, (2) a reduction in toxicity and (3) an ability of the vectors to overcome numerous biological barriers after systemic or local administration. Among the polycations presently used for gene delivery, poly(ethylene imine), PEI, takes a prominent position, due to its potential for endosomal escape. PEI as well as derivatives of PEI currently under investigation for DNA and RNA delivery will be discussed.
Criminal Network Analysis with Interactive Strategies: A Proof of Concept Study using Mobile Call Logs

The communication data are becoming increasingly important for criminal network analysis nowadays, this data provides a digital trace which can be regarded as a hidden clue to support the crack of criminal cases. Additionally, performing a timely and effective analysis on it can predict criminal intents and take efficient actions to restrain and prevent crimes. The primary work of our research is to suggest an analytical process with interactive strategies as a solution to the problem of characterizing criminal groups constructed from the communication data. It is expected to assist law enforcement agencies in the task of discovering the potential suspects and exploring the underlying structures of criminal network hidden behind the communication data. This process allows for network analysis with commonly used metrics to identify the core members. It permits exploration and visualization of the network in the goal of improving the comprehension of interesting microstructures. Most importantly, it also allows to extract community structures in a appropriate level with the label supervision strategy. Our work concludes illustrating the application of our interactive strategies to a real world criminal investigation with mobile call logs. Keywords-criminal network analysis; interactive strategy; network measure; community detection;
Problem of amputations in patients with newly diagnosed diabetes mellitus

A reduction of 50 % or more in diabetes‐related amputations is a primary target of the St Vincent Declaration. This is thought to be achievable because both primary and secondary preventative healthcare strategies are effective in reducing the incidence of diabetic foot ulceration and progression to amputation. Unfortunately there is a group who cannot benefit from preventative health care, that is, newly diagnosed diabetic patients with already established severe complications. Using our population‐based district diabetes information system we investigated, during the period 1 January 1992 to 31 December 96, the incidence and prevalence of lower extremity amputations (LEAs) and the proportion occurring in patients newly or recently diagnosed as having diabetes. Seventy‐nine diabetic patients (59 male, 20 female) were recorded as having had 94 LEAs, the incidence of diabetes‐related LEA being 475 per 100 000 diabetic patient‐years. Of these LEAs 16 (20.2 %) were performed within 1 year of diabetes being diagnosed. This study highlights an appreciable and previously unrecognized problem: patients presenting with established complications of diabetes who cannot benefit from secondary preventative healthcare. These patients pose a potential obstacle to achieving targets for reductions in diabetes‐related amputations. © 1998 John Wiley & Sons, Ltd.
Impact of upstream and downstream constraints on a signaling module’s ultrasensitivity

Much work has been done on the study of the biochemical mechanisms that result in ultrasensitive behavior of simple biochemical modules. However, in a living cell, such modules are embedded in a bigger network that constrains the range of inputs that the module will receive as well as the range of the module’s outputs that network will be able to detect. Here, we studied how the effective ultrasensitivity of a modular system is affected by these restrictions. We use a simple setup to explore to what extent the dynamic range spanned by upstream and downstream components of an ultrasensitive module impact on the effective sensitivity of the system. Interestingly, we found for some ultrasensitive motifs that dynamic range limitations imposed by downstream components can produce effective sensitivities much larger than that of the original module when considered in isolation.
Identification of the Hexon Region of an Adenovirus Involved in a New Outbreak of Keratoconjunctivitis

ABSTRACT We tested 15 adenovirus (Ad)-positive patients involved in a case of nosocomial spread of keratoconjunctivitis. A neutralization test, PCR-restriction fragment length polymorphism analysis, and sequencing of the hypervariable regions of the hexons were performed in order to identify the type of Ad involved. The serotype of the Ad was not identical to any published Ad sequence by either method.
Respiratory Complex I Dysfunction Due to Mitochondrial DNA Mutations Shifts the Voltage Threshold for Opening of the Permeability Transition Pore toward Resting Levels*

We have studied mitochondrial bioenergetics in HL180 cells (a cybrid line harboring the T14484C/ND6 and G14279A/ND6 mtDNA mutations of Leber hereditary optic neuropathy, leading to an ∼50% decrease of ATP synthesis) and XTC.UC1 cells (derived from a thyroid oncocytoma bearing a disruptive frameshift mutation in MT-ND1, which impairs complex I assembly). The addition of rotenone to HL180 cells and of antimycin A to XTC.UC1 cells caused fast mitochondrial membrane depolarization that was prevented by treatment with cyclosporin A, intracellular Ca2+ chelators, and antioxidant. Both cell lines also displayed an anomalous response to oligomycin, with rapid onset of depolarization that was prevented by cyclosporin A and by overexpression of Bcl-2. These findings indicate that depolarization by respiratory chain inhibitors and oligomycin was due to opening of the mitochondrial permeability transition pore (PTP). A shift of the threshold voltage for PTP opening close to the resting potential may therefore be the underlying cause facilitating cell death in diseases affecting complex I activity. This study provides a unifying reading frame for previous observations on mitochondrial dysfunction, bioenergetic defects, and Ca2+ deregulation in mitochondrial diseases. Therapeutic strategies aimed at normalizing the PTP voltage threshold may be instrumental in ameliorating the course of complex I-dependent mitochondrial diseases.
AlN Microresonator-Based Filters With Multiple Bandwidths at Low Intermediate Frequencies

Filters with various bandwidths at low intermediate frequency (IF) have been demonstrated using aluminum nitride (AlN) microresonator technology. Specifically, at 13 MHz, 6 kHz, and 25 kHz bandwidth filters were implemented using a single resonator topology, and 250 kHz and 500 kHz bandwidth filters were constructed via the parallel lattice topology using four sub-resonators and L-matching networks. The bandwidths of these filters are from 0.046% to 3.8%, and particularly the 500 kHz bandwidth filter at 13 MHz is wider than that of the resonator kt2 limit (40 kHz). The 100x variations in filter percent bandwidth were realized in a 1700 nm-thick aluminum nitride film on the same wafer through CMOS-compatible fabrication processes. Changes in the filter termination for proper filter matching were implemented in the Agilent Genesys RF and microwave design simulation software using actual measured filter responses with 50 Ω termination. The great flexibility in filter bandwidths and resonant frequencies, as well as other benefits such as size, manufacturing cost, isolation, and insertion loss provided by AlN microresonators will enable next generation multi-band, multi-waveform, and cognitive radios for defense and consumer wireless applications.
Evaluation of DNA vaccination with recombinant adenoviruses using bioluminescence imaging of antigen expression: impact of application routes and delivery with dendritic cells

Recombinant DNA vaccines are able to induce strong CD8+ T cell mediated immunity and have become increasingly attractive for the prevention and treatment of infectious diseases and cancer. Dendritic cells (DC), which critically control cellular immune responses, have been transduced with antigen ex vivo and used as ‘nature's adjuvant’ to enhance vaccine efficacy. The impact of the application route on the in vivo distribution of antigen and the stimulation of CD8+ T cells have been subjects of considerable debate. Here we report the construction of vectors expressing a fusion protein between EGFP, the H2‐Kb‐binding peptide OVAaa257−264 and green click beetle luciferase as a model antigen which allows for simultaneous quantitative assessment of antigen expression using fluorescence and bioluminescence imaging in correlation with CD8+ T cell stimulation in vivo. We applied this construct to evaluate DNA vaccination with recombinant adenoviral vectors, assess the impact of using cultured DC for vaccine delivery and investigate different application routes. Antigen expression was non‐invasively followed in vivo by visualizing bioluminescence with an ultrasensitive CCD camera. CD8+ T cell stimulation was detected with H2‐Kb‐OVAaa257−264 tetramers. We found that intravenous injection of adenovirus‐transduced DC stimulated the strongest OVAaa257−264‐specific cytotoxic T‐lymphocyte (CTL) responses although it delivered two orders of magnitude less antigen in vivo when compared to direct injection of recombinant adenovirus. We believe that our experimental approach has the potential to facilitate translational development of improved genetic immunization strategies targeting DC directly in vivo. Copyright © 2006 John Wiley & Sons, Ltd.