Miracle-dz/UniFAR-FTUs huggingface dataset:
Information-theoretically optimal compressed sensing via spatial coupling and approximate message passing

We study the compressed sensing reconstruction problem for a broad class of random, band-diagonal sensing matrices. This construction is inspired by the idea of spatial coupling in coding theory. As demonstrated heuristically and numerically by Krzakala et al. [11], message passing algorithms can effectively solve the reconstruction problem for spatially coupled measurements with undersampling rates close to the fraction of non-zero coordinates. We use an approximate message passing (AMP) algorithm and analyze it through the state evolution method. We give a rigorous proof that this approach is successful as soon as the undersampling rate δ exceeds the (upper) Rényi information dimension of the signal, d̅(pX). More precisely, for a sequence of signals of diverging dimension n whose empirical distribution converges to pX, reconstruction is with high probability successful from d̅(pX)n+o(n) measurements taken according to a band diagonal matrix. For sparse signals, i.e. sequences of dimension n and k(n) non-zero entries, this implies reconstruction from k(n) + o(n) measurements. For `discrete' signals, i.e. signals whose coordinates take a fixed finite set of values, this implies reconstruction from o(n) measurements. The result is robust with respect to noise, does not apply uniquely to random signals, but requires the knowledge of the empirical distribution of the signal pX.
Effects of human amniotic fluid on peripheral nerve scarring and regeneration in rats.

OBJECT Peripheral nerve repair surgery is still replete with challenges. Despite technical improvements in microsurgery, classic methods of nerve repair have failed to provide satisfactory results. The purpose of this study was to investigate the effects of amniotic fluid from humans on peripheral nerve scarring and regeneration in rats. METHODS Forty adult Sprague-Dawley rats were used in this study. After the right sciatic nerve in each rat was transected and repaired using an epineural suture procedure, the nerves were divided into two groups according to the solution applied around the repair site: experimental group, 0.3 ml human amniotic fluid (HAF); and control group, 0.3 ml saline. Macroscopic and histological evaluations of peripheral nerve scarring were performed 4 weeks postsurgery. Nerves treated with HAF demonstrated a significant reduction in the amount of scar tissue surrounding the repair site (p < 0.05). No evidence of a reaction against HAF was noted. Functional nerve regeneration was measured once every 2 weeks by using a sciatic function index until 12 weeks postsurgery. Functional recovery in nerves treated with amniotic fluid occurred significantly faster than that in nerves treated with saline (p < 0.05). Peripheral nerve regeneration was evaluated histomorphologically at 12 weeks postsurgery. Nerves treated with amniotic fluid showed significant improvement with respect to the indices of fiber maturation (p < 0.05). CONCLUSIONS Preliminary data show that HAF enhances peripheral nerve regeneration. The preventive effect of HAF on epineural scarring and the rich content of neurotrophic and neurite-promoting factors possibly contribute to this result.
Histological studies on the marsupium of two terrestrial isopods (Crustacea, Isopoda, Oniscidea)

Abstract The marsupium, a brood pouch in peracarid crustaceans (Crustacea, Malacostraca) has evolved in terrestrial environment for providing nutrition and optimal conditions for embryogenesis. In the present study we give details on the histology and ultrastructure of its constituting elements such as oostegites and cotyledons. Marsupia of two different eco-morphological types of woodlice, namely the non-conglobating species Trachelipus rathkii Brandt, 1833 and the conglobating species Cylisticus convexus De Geer, 1778 were investigated. Light microscopic (LM) studies showed some differences in the main structure of the two species’ brood pouch: in Trachelipus rathkii, a ‘clinger’ type woodlice, the oostegites bend outwards during brood incubation as growing offspring require more space, while in Cylisticus convexus, a ‘roller’ type isopod, the sternites arch into the body cavity to ensure space for developing offspring and still allowing conglobation of the gravid females. The quantitative analysis of the oostegites’ cuticle proved that the outer part is about 2.5 - 3 times thicker compared to the inner part in both species. Electron microscopic (TEM) examinations show only small histological differences in the oostegites and cotyledon structure of the two species. Cellular elements and moderately electron dense fleecy precipitate are found in the hemolymph space between the two cuticles of oostegites. The cells contain PAS positive polysaccharide areas. TEM studies revealed some differences in the cotyledon ultrastructure of the two species. Cotyledons of Trachelipus rathkii consist of cells with cristate mitochondria and granular endoplasmic reticulum with cisterns. Cotyledons of Cylisticus convexus consist of cells with densely cristate mitochondria and ribosomes attached to vesicular membrane structures. In both species cells with electron dense bodies were observed. We conclude that - besides the differences in marsupial shapes - the fine structure of the oostegites and cotyledons is hardly affected by the eco-morphological type, specifically the conglobating or non-conglobating character of the studied species.
Nonlinear Channel Equalization With Gaussian Processes for Regression

We propose Gaussian processes for regression (GPR) as a novel nonlinear equalizer for digital communications receivers. GPR's main advantage, compared to previous nonlinear estimation approaches, lies on their capability to optimize the kernel hyperparameters by maximum likelihood, which improves its performance significantly for short training sequences. Besides, GPR can be understood as a nonlinear minimum mean square error estimator, a standard criterion for training equalizers that trades off the inversion of the channel and the amplification of the noise. In the experiment section, we show that the GPR-based equalizer clearly outperforms support vector machine and kernel adaline approaches, exhibiting outstanding results for short training sequences.
Optimized T1-MPRAGE Sequence for Better Visualization of Spinal Cord Multiple Sclerosis Lesions at 3T

BACKGROUND AND PURPOSE: Spinal cord lesions are highly prevalent in MS, and their visualization can help both in diagnosis and patient follow-up. However, the sensitivity of MR imaging to spinal cord lesions remains poor, primarily because of suboptimal contrast between lesions and a normal-appearing cord. Here, we propose an optimized 3D MPRAGE sequence for improved detection of MS lesions in the spinal cord at 3T. MATERIALS AND METHODS: Images were acquired by use of T2 FSE, STIR, T1-gradient recalled-echo (for T1 mapping), and T1-MPRAGE in the sagittal plane, and T2*-weighted scans in the axial plane, on 40 patients with MS and 7 healthy volunteers. Two observers qualitatively evaluated the images for lesion conspicuity. Lesions seen between the C1 and C4 segments in 10 randomly selected patients with MS were further evaluated quantitatively for contrast-to-noise ratio between the lesion and normal-appearing cord, and for lesion burden. RESULTS: Spinal cord lesions were more conspicuous on the optimized T1-MPRAGE sequence than on any other sequence tested. Detailed analysis revealed that lesions were almost 3 times more conspicuous (P < .01), and the total lesion volume was 2 times greater (P < .05, n=10), in the T1-MPRAGE sequence compared with the standard STIR sequence. Correlation of clinical disability (Expanded Disability Status Score) with lesion load from each sequence also demonstrated the importance of the improved lesion conspicuity with T1-MPRAGE. CONCLUSIONS: The optimized T1-MPRAGE sequence described here improves the reliability of lesion visualization and estimation of lesion burden, especially when used in conjunction with other well-established clinical sequences.
Zero overhead watermarking technique for FPGA designs

FPGAs, because of their re-programmability, are becoming very popular for creating and exchanging VLSI intellectual properties (IPs) in the reuse-based design paradigm. Existing watermarking and fingerprinting techniques successfully embed identification information into FPGA designs to deter IP infringement. However, such methods incur timing and/or resource overhead, unpredictable at times, which causes performance degradation. In this paper, we propose a new FPGA watermarking technique that guarantees zero design overhead.Our approach consists of two phases. First we design as usual to obtain the best, possible, quality IP. Then we map the required signature to additional timing constraints on carefully selected nets and redo a small portion of the design (e.g. place and route). The FPGA configuration bitstream for the resulting watermarked design will be significantly different from the original design, which provides us with a strong proof of authorship. The watermarking technique has zero design overhead because it is developed to maintain the performance of the design from the first phase. This is demonstrated by applying the proposed technique on several real-life FPGA designs, which range in size from a few thousand to more than two million gates, on Xilinx devices.
A global-to-local approach for robust range image segmentation

We present a range image segmentation algorithm based on a robust estimation technique, the M-estimator sample consensus (MSAC). The algorithm is a parallelizable "global-to-local" approach for the extraction of planar surfaces directly from range images. Solutions to some problems faced when extracting planar surfaces globally are also proposed. Experimental results show the algorithm is robust to image noise in the sense that it is able to preserve object shapes so that neither presmoothing, nor postprocessing steps are required. It also does not rely on MSAC and can be easily adapted to use other robust estimators. Thus, it may be used as a framework to compare robust estimators.
Structural Characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole

Background Chagas Disease is the leading cause of heart failure in Latin America. Current drug therapy is limited by issues of both efficacy and severe side effects. Trypansoma cruzi, the protozoan agent of Chagas Disease, is closely related to two other major global pathogens, Leishmania spp. , responsible for leishmaniasis, and Trypansoma brucei, the causative agent of African Sleeping Sickness. Both T. cruzi and Leishmania parasites have an essential requirement for ergosterol, and are thus vulnerable to inhibitors of sterol 14α-demethylase (CYP51), which catalyzes the conversion of lanosterol to ergosterol. Clinically employed anti-fungal azoles inhibit ergosterol biosynthesis in fungi, and specific azoles are also effective against both Trypanosoma and Leishmania parasites. However, modification of azoles to enhance efficacy and circumvent potential drug resistance has been problematic for both parasitic and fungal infections due to the lack of structural insights into drug binding. Methodology/Principal Findings We have determined the crystal structures for CYP51 from T. cruzi (resolutions of 2.35 Å and 2.27 Å), and from the related pathogen T. brucei (resolutions of 2.7 Å and 2.6 Å), co-crystallized with the antifungal drugs fluconazole and posaconazole. Remarkably, both drugs adopt multiple conformations when binding the target. The fluconazole 2,4-difluorophenyl ring flips 180° depending on the H-bonding interactions with the BC-loop. The terminus of the long functional tail group of posaconazole is bound loosely in the mouth of the hydrophobic substrate binding tunnel, suggesting that the major contribution of the tail to drug efficacy is for pharmacokinetics rather than in interactions with the target. Conclusions/Significance The structures provide new insights into binding of azoles to CYP51 and mechanisms of potential drug resistance. Our studies define in structural detail the CYP51 therapeutic target in T. cruzi, and offer a starting point for rationally designed anti-Chagasic drugs with improved efficacy and reduced toxicity.
Cannabinoid Receptor 2 Signaling Does Not Modulate Atherogenesis in Mice

Background Strong evidence supports a protective role of the cannabinoid receptor 2 (CB2) in inflammation and atherosclerosis. However, direct proof of its involvement in lesion formation is lacking. Therefore, the present study aimed to characterize the role of the CB2 receptor in Murine atherogenesis. Methods and Findings Low density lipoprotein receptor-deficient (LDLR−/−) mice subjected to intraperitoneal injections of the selective CB2 receptor agonist JWH-133 or vehicle three times per week consumed high cholesterol diet (HCD) for 16 weeks. Surprisingly, intimal lesion size did not differ between both groups in sections of the aortic roots and arches, suggesting that CB2 activation does not modulate atherogenesis in vivo. Plaque content of lipids, macrophages, smooth muscle cells, T cells, and collagen were also similar between both groups. Moreover, CB2 −/−/LDLR−/− mice developed lesions of similar size containing more macrophages and lipids but similar amounts of smooth muscle cells and collagen fibers compared with CB2 +/+/LDLR−/− controls. While JWH-133 treatment reduced intraperitoneal macrophage accumulation in thioglycollate-illicited peritonitis, neither genetic deficiency nor pharmacologic activation of the CB2 receptor altered inflammatory cytokine expression in vivo or inflammatory cell adhesion in the flow chamber in vitro. Conclusion Our study demonstrates that both activation and deletion of the CB2 receptor do not relevantly modulate atherogenesis in mice. Our data do not challenge the multiple reports involving CB2 in other inflammatory processes. However, in the context of atherosclerosis, CB2 does not appear to be a suitable therapeutic target for reduction of the atherosclerotic plaque.
Gametogenesis Eliminates Age-Induced Cellular Damage and Resets Life Span in Yeast

When yeast commits to sex, reversal of age-induced cellular damage rejuvenates its life span. Eukaryotic organisms age, yet detrimental age-associated traits are not passed on to progeny. How life span is reset from one generation to the next is not known. We show that in budding yeast resetting of life span occurs during gametogenesis. Gametes (spores) generated by aged cells show the same replicative potential as gametes generated by young cells. Age-associated damage is no longer detectable in mature gametes. Furthermore, transient induction of a transcription factor essential for later stages of gametogenesis extends the replicative life span of aged cells. Our results indicate that gamete formation brings about rejuvenation by eliminating age-induced cellular damage.
Reduced hippocampal volumes associated with the long variant of the tri‐ and diallelic serotonin transporter polymorphism in major depression

Substantial evidence supports a role for dysfunction of the serotonin transporter (5‐HTT) in the pathogenesis of major depression. The polymorphism of the serotonin transporter gene (5‐HTTLPR) was found to be associated with reduced hippocampal volume in major depression. However, the original diallelic polymorphism was criticized, because the L‐allele can be subtyped into La and Lg alleles, the latter of which is thought to be similar to the S‐allele. Therefore, the study aim was to examine the influences of the triallelic (La‐Lg‐S system) and diallelic 5‐HTTLPR on hippocampal volumes in patients with major depression and healthy controls. Using high‐resolution MRI hippocampal volumes and polymorphisms (5‐HTTLPR) were measured in 60 in‐patients with major depression and 60 healthy controls. Patients with the La/La genotype had significantly smaller hippocampal gray and white matter than La/La controls. No significant differences were found between patients and controls with La/(Lg + S) or (Lg + S)/(Lg + S) genotype. Moreover, within the patient group the La/La homozygous genotype had significantly smaller hippocampal white matter volumes than the La/(Lg + S) or (Lg + S)/(Lg + S) genotype. In conclusion, with the diallelic as well as the triallelic system the homozygosity for the long‐allele is associated with decreased hippocampal volumes in patients with major depression, but not in healthy controls, suggesting that disease or stress specific processes linked to the serotonergic system may enhance the vulnerability to morphological alterations. © 2008 Wiley‐Liss, Inc.
Impact of tumor-specific targeting on the biodistribution and efficacy of siRNA nanoparticles measured by multimodality in vivo imaging

Targeted delivery represents a promising approach for the development of safer and more effective therapeutics for oncology applications. Although macromolecules accumulate nonspecifically in tumors through the enhanced permeability and retention (EPR) effect, previous studies using nanoparticles to deliver chemotherapeutics or siRNA demonstrated that attachment of cell-specific targeting ligands to the surface of nanoparticles leads to enhanced potency relative to nontargeted formulations. Here, we use positron emission tomography (PET) and bioluminescent imaging to quantify the in vivo biodistribution and function of nanoparticles formed with cyclodextrin-containing polycations and siRNA. Conjugation of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid to the 5′ end of the siRNA molecules allows labeling with 64Cu for PET imaging. Bioluminescent imaging of mice bearing luciferase-expressing Neuro2A s.c. tumors before and after PET imaging enables correlation of functional efficacy with biodistribution data. Although both nontargeted and transferrin-targeted siRNA nanoparticles exhibit similar biodistribution and tumor localization by PET, transferrin-targeted siRNA nanoparticles reduce tumor luciferase activity by ≈50% relative to nontargeted siRNA nanoparticles 1 d after injection. Compartmental modeling is used to show that the primary advantage of targeted nanoparticles is associated with processes involved in cellular uptake in tumor cells rather than overall tumor localization. Optimization of internalization may therefore be key for the development of effective nanoparticle-based targeted therapeutics.
Cervical cancer awareness and preventive practices: a challenge for female urban slum dwellers in Lagos, Nigeria.

Cervical cancer is the commonest gynaecological cancer in Nigeria and women of low socio-economic status are at high risk of this condition. A study was conducted on the awareness of cervical cancer, attitude towards the disease and screening practice of women residing in two urban slums of Lagos, Nigeria. It also determined the prevalence of major risk factors for cervical cancer among the women. Multistage sampling was used to select 240 women who were interviewed with a structured questionnaire and data collected was analyzed with Epi-info version 3.5. 1 statistical software. Only 10 (4.2%) women in this study were aware of cervical cancer and none of them believed they were at risk of developing the disease. Most (73.3%) were willing to undergo a cervical cancer screening test. Age, education and previous history of vaginal examination were positively associated with willingness to undergo screening (p < 0.05). The respondents had a high prevalence of major risk factors for cervical cancer such as early age at sexual debut, multiple sexual partners and male partner with other female partners. Efforts need to be intensified to increase awareness of this condition and to promote low-cost cervical cancer screening among this underserved population.
5-Hydroxytryptophan during critical postnatal period improves cognitive performances and promotes dendritic spine maturation in genetic mouse model of phenylketonuria

Although phenylketonuria (PKU) is the most common genetic cause of mental retardation, the cellular mechanisms underlying impaired brain function are still unclear. Using PAHenu2 mice (ENU2), the genetic mouse model of PKU, we previously demonstrated that high phenylalanine levels interfere with brain tryptophan hydroxylase activity by reducing the availability of serotonin (5-hydroxytryptamine, 5-HT), crucial for maturation of neuronal connectivity in the prefrontal cortex (PFC), around the third postnatal week, a critical period for cortical maturation. 5-Hydroxytryptophan (5-HTP), the product of tryptophan hydroxylation, is known to be a better treatment to increase brain 5-HT levels. In this study we investigated the role of 5-HT during the early postnatal period in cognitive disturbances and in cortical dendritic alterations of PKU subjects by restoring temporarily (postnatal days 14–21) physiological brain levels of 5-HT in ENU2 through 5-HTP treatment. In adult ENU2 mice early 5-HTP treatment reverses cognitive deficits in spatial and object recognition tests accompanied by an increase in spine maturation of pyramidal neurons in layer V of the prelimbic/infralimbic area of the PFC, although locomotor deficits are not recovered by treatment. Taken together, our results support the hypothesis that mental retardation in PKU depends on reduced availability of brain 5-HT during critical developmental periods that interferes with cortical maturation and point to 5-HTP supplementation as a highly promising additional tool to heal PKU patients.
Altered functional connectivity of brainstem nuclei in new daily persistent headache: Evidence from resting‐state functional magnetic resonance imaging

Abstract Objectives The new daily persistent headache (NDPH) is a rare primary headache disorder. However, the underlying mechanisms of NDPH remain incompletely understood. This study aims to apply seed‐based analysis to explore the functional connectivity (FC) of brainstem nuclei in patients with NDPH using resting‐state functional magnetic resonance imaging (MRI). Methods The FC analysis from the region of interest (ROI) to whole brain voxels was used to investigate 29 patients with NDPH and 37 well‐matched healthy controls (HCs) with 3.0 Tesla MRI. The 76 nuclei in the brainstem atlas were defined as ROIs. Furthermore, we explored the correlations between FC and patients' clinical characteristics and neuropsychological evaluations. Results Patients with NDPH exhibited reduced FC in multiple brainstem nuclei compared to HCs (including right inferior medullary reticular formation, right mesencephalic reticular formation, bilateral locus coeruleus, bilateral laterodorsal tegmental nucleus‐central gray of the rhombencephalon, median raphe, left medial parabrachial nucleus, periaqueductal gray, and bilateral ventral tegmental area‐parabrachial pigmented nucleus complex) and increased FC in periaqueductal gray. No significant correlations were found between the FC of these brain regions and clinical characteristics or neuropsychological evaluations after Bonferroni correction (p > 0.00016). Conclusions Our results demonstrated that patients with NDPH have abnormal FC of brainstem nuclei involved in the perception and regulation of pain and emotions.
The Effectiveness of Dictionary and Web-Based Answer Reranking

We describe an in-depth study of using a dictionary (WordNet) and web search engines (Altavista, MSN, and Google) to boost the performance of an automated question answering system, Webclopedia, in answering definition questions. The results indicate applying dictionary and web-based answer reranking together increase the performance of Webclopedia on a set of 102 TREC-10 definition questions by 25% in mean reciprocal rank score and 14% in finding answers in the top 5.