Built-In Self-Test of Programmable Resources in Microcontroller Based System-on-Chips

System-on-Chip (SoC) implementations typically incorporate embedded Field Programmable Gate Array (FPGA) cores to take advantage of the programmable logic and routing resources provided by FPGAs. Testing the FPGA core typically requires numerous configuration downloads to completely test the various modes of operation of the programmable logic resources and the size of each configuration download file is large due to large amount of programmable resources. However, the ability to perform dynamic partial reconfiguration of the FPGA core from embedded processor core opens new opportunities for testing the FPGA using Built-In Self-Test (BIST). This thesis discusses the implementation of BIST for FPGA cores using partial dynamic reconfiguration from the embedded processor. As a result, all external configuration downloads are eliminated and replaced by one single processor program that programs the FPGA core for BIST, executes the BIST sequence, retrieves the BIST results, and executes diagnostic procedures to locate and identify faults detected by the BIST. Total testing time is improved by as much as a factor of 45 and a configuration memory storage requirement by as much as a factor of 83 by using dynamic partial reconfiguration compared to the traditional approach that requires BIST configuration downloads for every mode of operation of the programmable logic resources in the FPGA core of the Atmel AT94K series SoCs

Development of prognostic signatures for intermediate-risk papillary thyroid cancer

BACKGROUND: The incidence of Papillary thyroid carcinoma (PTC), the most common type of thyroid malignancy, has risen rapidly worldwide. PTC usually has an excellent prognosis. However, the rising incidence of PTC, due at least partially to widespread use of neck imaging studies with increased detection of small cancers, has created a clinical issue of overdiagnosis, and consequential overtreatment. We investigated how molecular data can be used to develop a prognostics signature for PTC. METHODS: The Cancer Genome Atlas (TCGA) recently reported on the genomic landscape of a large cohort of PTC cases. In order to decrease unnecessary morbidity associated with over diagnosing PTC patient with good prognosis, we used TCGA data to develop a gene expression signature to distinguish between patients with good and poor prognosis. We selected a set of clinical phenotypes to define an ‘extreme poor’ prognosis group and an ‘extreme good’ prognosis group and developed a gene signature that characterized these. RESULTS: We discovered a gene expression signature that distinguished the extreme good from extreme poor prognosis patients. Next, we applied this signature to the remaining intermediate risk patients, and show that they can be classified in clinically meaningful risk groups, characterized by established prognostic disease phenotypes. Analysis of the genes in the signature shows many known and novel genes involved in PTC prognosis. CONCLUSIONS: This work demonstrates that using a selection of clinical phenotypes and treatment variables, it is possible to develop a statistically useful and biologically meaningful gene signature of PTC prognosis, which may be developed as a biomarker to help prevent overdiagnosis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-016-2771-6) contains supplementary material, which is available to authorized users

Epigenetically Mediated Pathogenic Effects of Phenanthrene on Regulatory T Cells

Phenanthrene (Phe), a polycyclic aromatic hydrocarbon (PAH), is a major constituent of urban air pollution. There have been conflicting results regarding the role of other AhR ligands 2,3,7,8- tetrachlorodibenzo-p-dioxin (TCDD) and 6-formylindolo [3,2-b]carbazole (FICZ) in modifying regulatory T cell populations (Treg) or T helper (Th)17 differentiation, and the effects of Phe have been understudied. We hypothesized that different chemical entities of PAH induce Treg to become either Th2 or Th17 effector T cells through epigenetic modification of FOXP3. To determine specific effects on T cell populations by phenanthrene, primary human Treg were treated with Phe, TCDD, or FICZ and assessed for function, gene expression, and phenotype. Methylation of CpG sites within the FOXP3 locus reduced FOXP3 expression, leading to impaired Treg function and conversion of Treg into a CD4+CD25lo Th2 phenotype in Phe-treated cells. Conversely, TCDD treatment led to epigenetic modification of IL-17A and conversion of Treg to Th17 T cells. These findings present a mechanism by which exposure to AhR-ligands mediates human T cell responses and begins to elucidate the relationship between environmental exposures, immune modulation, and initiation of human disease

Intraoperative cerebral hemodynamic monitoring during carotid endarterectomy via diffuse correlation spectroscopy and near-infrared spectroscopy

Objective: This pilot study aims to show the feasibility of noninvasive and real-time cerebral hemodynamic monitoring during carotid endarterectomy (CEA) via diffuse correlation spectroscopy (DCS) and near-infrared spectroscopy (NIRS). Methods: Cerebral blood flow index (CBFi) was measured unilaterally in seven patients and bilaterally in seventeen patients via DCS. In fourteen patients, hemoglobin oxygenation changes were measured bilaterally and simultaneously via NIRS. Cerebral autoregulation (CAR) and cerebrovascular resistance (CVR) were estimated using CBFi and arterial blood pressure data. Further, compensatory responses to the ipsilateral hemisphere were investigated at different contralateral stenosis levels. Results: Clamping of carotid arteries caused a sharp increase of CVR (~70%) and a marked decrease of ipsilateral CBFi (57%). From the initial drop, we observed partial recovery in CBFi, an increase of blood volume, and a reduction in CVR in the ipsilateral hemisphere. There were no significant changes in compensatory responses between different contralateral stenosis levels as CAR was intact in both hemispheres throughout the CEA phase. A comparison between hemispheric CBFi showed lower ipsilateral levels during the CEA and post-CEA phases (p &lt; 0.001, 0.03). Conclusion: DCS alone or combined with NIRS is a useful monitoring technique for real-time assessment of cerebral hemodynamic changes and allows individualized strategies to improve cerebral perfusion during CEA by identifying different hemodynamic metrics.</p

Towards multiomic analysis of oral mucosal pathologies

Oral mucosal pathologies comprise an array of diseases with worldwide prevalence and medical relevance. Affecting a confined space with crucial physiological and social functions, oral pathologies can be mutilating and drastically reduce quality of life. Despite their relevance, treatment for these diseases is often far from curative and remains vastly understudied. While multiple factors are involved in the pathogenesis of oral mucosal pathologies, the host's immune system plays a major role in the development, maintenance, and resolution of these diseases. Consequently, a precise understanding of immunological mechanisms implicated in oral mucosal pathologies is critical (1) to identify accurate, mechanistic biomarkers of clinical outcomes; (2) to develop targeted immunotherapeutic strategies; and (3) to individualize prevention and treatment approaches. Here, we review key elements of the immune system's role in oral mucosal pathologies that hold promise to overcome limitations in current diagnostic and therapeutic approaches. We emphasize recent and ongoing multiomic and single-cell approaches that enable an integrative view of these pathophysiological processes and thereby provide unifying and clinically relevant biological signatures

Sickle Cell Disease Subjects Have a Distinct Abnormal Autonomic Phenotype Characterized by Peripheral Vasoconstriction With Blunted Cardiac Response to Head-Up Tilt

In sickle cell disease (SCD), prolonged capillary transit times, resulting from reduced peripheral blood flow, increase the likelihood of rigid red cells entrapment in the microvasculature, predisposing to vaso-occlusive crisis. Since changes in peripheral flow are mediated by the autonomic nervous system (ANS), we tested the hypothesis that the cardiac and peripheral vascular responses to head-up tilt (HUT) are abnormal in SCD. Heart rate, respiration, non-invasive continuous blood pressure and finger photoplethysmogram (PPG) were monitored before, during, and after HUT in SCD, anemic controls and healthy subjects. Percent increase in heart rate from baseline was used to quantify cardiac ANS response, while percent decrease in PPG amplitude represented degree of peripheral vasoconstriction. After employing cluster analysis to determine threshold levels, the HUT responses were classified into four phenotypes: (CP) increased heart rate and peripheral vasoconstriction; (C) increased heart rate only; (P) peripheral vasoconstriction only; and (ST) subthreshold cardiac and peripheral vascular responses. Multinomial logistic regression (MLR) was used to relate these phenotypic responses to various parameters representing blood properties and baseline cardiovascular activity. The most common phenotypic response, CP, was found in 82% of non-SCD subjects, including those with chronic anemia. In contrast, 70% of SCD subjects responded abnormally to HUT: C-phenotype = 22%, P-phenotype = 37%, or ST-phenotype = 11%. MLR revealed that the HUT phenotypes were significantly associated with baseline cardiac parasympathetic activity, baseline peripheral vascular variability, hemoglobin level and SCD diagnosis. Low parasympathetic activity at baseline dramatically increased the probability of belonging to the P-phenotype in SCD subjects, even after adjusting for hemoglobin level, suggesting a characteristic autonomic dysfunction that is independent of anemia. Further analysis using a mathematical model of heart rate variability revealed that the low parasympathetic activity in P-phenotype SCD subjects was due to impaired respiratory-cardiac coupling rather than reduced cardiac baroreflex sensitivity. By having strong peripheral vasoconstriction without compensatory cardiac responses, P-phenotype subjects may be at increased risk for vaso-occlusive crisis. The classification of autonomic phenotypes based on HUT response may have potential use for guiding therapeutic interventions to alleviate the risk of adverse outcomes in SCD

Mental stress causes vasoconstriction in subjects with sickle cell disease and in normal controls

Vaso-occlusive crisis (VOC) is a hallmark of sickle cell disease (SCD) and occurs when deoxygenated sickled red blood cells occlude the microvasculature. Any stimulus, such as mental stress, which decreases microvascular blood flow will increase the likelihood of red cell entrapment resulting in local vaso-occlusion and progression to VOC. Neurally mediated vasoconstriction might be the physiological link between crisis triggers and vaso-occlusion. In this study, we determined the effect of mental stress on microvascular blood flow and autonomic nervous system reactivity. Sickle cell patients and controls performed mentally stressful tasks, including a memory task, conflict test and pain anticipation test. Blood flow was measured using photoplethysmography, autonomic reactivity was derived from electrocardiography and perceived stress was measured by the State-Trait Anxiety Inventory questionnaire. Stress tasks induced a significant decrease in microvascular blood flow, parasympathetic withdrawal and sympathetic activation in all subjects. Of the various tests, pain anticipation caused the highest degree of vasoconstriction. The magnitude of vasoconstriction, sympathetic activation and perceived stress was greater during the Stroop conflict test than during the N-back memory test, indicating the relationship between magnitude of experimental stress and degree of regional vasoconstriction. Baseline anxiety had a significant effect on the vasoconstrictive response in sickle cell subjects but not in controls. In conclusion, mental stress caused vasoconstriction and autonomic nervous system reactivity in all subjects. Although the pattern of responses was not significantly different between the two groups, the consequences of vasoconstriction can be quite significant in SCD because of the resultant entrapment of sickle cells in the microvasculature. This suggests that mental stress can precipitate a VOC in SCD by causing neural-mediated vasoconstriction

Relationships of Mental Disorders and Weight Status in the Korean Adult Population

The purpose of this study was to evaluate the associations between weight status and mental disorders, including depressive disorder, anxiety disorder and alcohol use disorder. A total of nationally representative 6,510 subjects aged 18-64 yr was interviewed in face-to-face household survey. Response rate was 81.7%. Mental disorders were diagnosed using the Korean version of the Composite International Diagnostic Interview (K-CIDI). The subjects reported their heights and weights. After adjusting for age and gender, the lifetime diagnosis of depressive disorder had a significant association with only the underweight group (odds ratio [OR], 1.68, 95% confidence interval [CI], 1.19-2.38). The association between underweight and depressive disorder was the strongest for subjects with a high education level (OR, 1.75, 95% CI, 1.2-2.56), subjects with a married/cohabiting status (OR, 1.94, 95% CI, 1.17-3.22) and smokers (OR, 2.58, 95% CI, 1.33-4.98). There was no significant association between obesity and depressive disorder in Korea. But there was a significant association between the underweight group and depressive disorder. The relationship between obesity and mental disorder in a Korean population was different from that in a Western population. These results suggest that the differences of traditional cultures and races might have an important effect on the associations between the weight status and mental disorders

The Firre locus produces a trans -acting RNA molecule that functions in hematopoiesis

Abstract: RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis

Wireless, battery-free, remote photoactivation of caged-morphine for photopharmacological pain modulation without side effects

Chronic pain severely impairs physical, psychological, and cognitive functions. While opioid-based therapies can be effective, they are limited by tolerance, dependence, and adverse side effects, highlighting the need for safer alternatives. Recent advances in photopharmacology allow precise modulation of pain-related neuronal circuits, offering improved control and effectiveness. For delivery of light, fully implantable, wireless, battery-free optical systems in miniaturized forms offer attractive options relative to alternatives that use conventional bulk hardware and fiber optic tethers. This work presents a technology of this type, based on microscale light-emitting diodes (μ-ILEDs) and near-field communication (NFC) protocols, and optimized to activate photocaged morphine (pc-Mor) in targeted regions of the spinal cord. The unique flexible, lightweight designs ensure stable, minimally invasive operation in small animal model behavioral studies, with efficient power consumption and minimized thermal load on fragile tissues. Experimental results demonstrate effective pain suppression and reduced opioid-related side effects in an animal model of pain, thereby establishing this platform as a promising solution for chronic pain management.This work was funded by the Querrey-Simpson Institute for Bioelectronics. This work was also supported by FEDER/Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación (PID2023-147425OB-I00 to FC, PID2020-120499RB-I00 to AL) and Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) - Generalitat de Catalunya (projects 2021 SGR 00698 to FC, 2021 SGR 00064 to JH, 2021 SGR 00508 to AL).Peer reviewe