Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Power Consumption and Linearity in Capacitive Digital-to-Analog Converters Used in Successive Approximation ADCs

Successive-approximation analog-to-digital converters (SA-ADCs) are widely used in ultra-low-power applications. In this paper, the power consumption and the linearity of capacitive-array digital-to-analog converters (DACs) employed in SA-ADCs are analyzed. Specifically, closed-form formulas for the power consumption as well as the standard deviation of INL and DNL for three commonly-used radix-2 architectures including the effect of parasitic capacitances are presented and the structures are compared. The proposed analysis can be employed in choosing the best architecture and optimizing it in both hand calculations and computer-aided-design tools. Measurement results of previously published works as well as simulation results of a 10-bit 10 kS/s SA-ADC confirm the accuracy of the proposed equations. It will be shown that, in spite of what commonly is assumed, although the total capacitance and the power consumption of those architectures employing attenuating capacitors seem to be smaller than conventional binary-weighted structures, the linearity requirements impose much larger unit capacitance to the structure such that the entire power consumption is larger.
Molecular Phylogeny and Biogeographic History of the Armored Neotropical Catfish Subfamilies Hypoptopomatinae, Neoplecostominae and Otothyrinae (Siluriformes: Loricariidae)

The main objectives of this study are estimate a species-dense, time-calibrated molecular phylogeny of Hypoptopomatinae, Neoplecostominae, and Otothyrinae, which together comprise a group of armoured catfishes that is widely distributed across South America, to place the origin of major clades in time and space, and to demonstrate the role of river capture on patterns of diversification in these taxa. We used maximum likelihood and Bayesian methods to estimate a time-calibrated phylogeny of 115 loricariid species, using three mitochondrial and one nuclear genes to generate a matrix of 4,500 base pairs, and used parametric biogeographic analyses to estimate ancestral geographic ranges and to infer the effects of river capture events on the geographic distributions of these taxa. Our analysis recovered Hypoptopomatinae, Neoplecostominae, and Otothyrinae as monophyletic with strong statistical support, and Neoplecostominae as more closely related to Otothyrinae than to Hypoptopomatinae. Our time-calibrated phylogeny and ancestral-area estimations indicate an origin of Hypoptopomatinae, Neoplecostominae, and Otothyrinae during the Lower Eocene in the Atlantic Coastal Drainages, from which it is possible to infer several dispersal events to adjacent river basins during the Neogene. In conclusion we infer a strong influence of river capture in: (1) the accumulation of modern clade species-richness values; (2) the formation of the modern basin-wide species assemblages, and (3) the presence of many low-diversity, early-branching lineages restricted to the Atlantic Coastal Drainages. We further infer the importance of headwater stream capture and marine transgressions in shaping patterns in the distributions of Hypoptopomatinae, Neoplecostominae and Otothyrinae throughout South America.
Functional Implications of MicroRNAs in Crohn’s Disease Revealed by Integrating MicroRNA and Messenger RNA Expression Profiling

Crohn’s disease (CD) is a debilitating inflammatory bowel disease (IBD) that emerges due to the influence of genetic and environmental factors. microRNAs (miRNAs) have been identified in the tissue and sera of IBD patients and may play an important role in the induction of IBD. Our study aimed to identify differentially expressed miRNAs and miRNAs with the ability to alter transcriptome activity by comparing inflamed tissue samples with their non-inflamed counterparts. We studied changes in miRNA–mRNA interactions associated with CD by examining their differential co-expression relative to normal mucosa from the same patients. Correlation changes between the two conditions were incorporated into scores of predefined gene sets to identify biological processes with altered miRNA-mediated control. Our study identified 28 miRNAs differentially expressed (p-values < 0.01), of which 14 are up-regulated. Notably, our differential co-expression analysis highlights microRNAs (i.e., miR-4284, miR-3194 and miR-21) that have known functional interactions with key mechanisms implicated in IBD. Most of these miRNAs cannot be detected by differential expression analysis that do not take into account miRNA–mRNA interactions. The identification of differential miRNA–mRNA co-expression patterns will facilitate the investigation of the miRNA-mediated molecular mechanisms underlying CD pathogenesis and could suggest novel drug targets for validation.
Disparities in cancer outcomes in regional and rural Australia

Cancer in Australia is largely a positive story. Despite increased incidence rates, which reflect an ageing population, the corresponding falling age-adjusted death rates and better survival suggest a health system well-equipped for early detection and treatment of cancer. However, there are inequalities in cancer survival among people in rural, regional and remote areas of Australia and disparities in cancer treatment, particularly in respect to colorectal, lung and breast cancer, are probably partly responsible. Other factors closely aligned with cancer risk and poorer survival in regional and remote Australia include: greater levels of socio-economic disadvantage, limited access to specialist cancer treatment services and a greater proportion of Indigenous people who have their cancers diagnosed at more advanced stages and may receive poorer treatment. In the absence of more complete data, the survival pattern we see in remote parts of Australia probably represents the cancer experience of Indigenous Australians. Questions about the ways in which all of these factors collectively explain the survival picture in Australia will remain unanswered, unless we enrich our data sources, enhance cancer surveillance and work to better understand how the health system responds to the needs of different population subgroups, in particular our Indigenous people.
Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina

Abstract Background: Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. Aim: Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations. Subjects and methods: The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses. Results: The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations. Conclusion: These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.
Neuropsychiatric Symptoms and Cognitive Impairment: Understanding the Importance of Co-Morbid Symptoms.

BACKGROUND Neuropsychiatric symptoms (NPS) are common in older adults with cognitive impairment, yet little is known about population-based prevalence and clinical implications of co-morbid symptom presentation across the spectrum from normal cognition to dementia. OBJECTIVE To characterize the prevalence of NPS and explore the clinical implications of co-morbid symptom presentation. METHODS Cross-sectional study of 1,417 older adults (aged 73-79) with dementia (n = 40); with mild cognitive impairment (MCI; n = 133); who are 'cognitively normal, but-at-risk' (CN-AR; n = 397); and who are cognitively normal (n = 847). NPS were assessed by the Neuropsychiatric Inventory. Cluster analyses were conducted using a latent class analysis (LCA). RESULTS NPS are highly prevalent across the cognitive function spectrum (30.8% -80%). NPS were associated with a 3-fold increased risk of dementia, a 2-fold increased risk of MCI, and a 1.5-times increased risk of CN-AR. Each additional co-morbid symptom was associated with an additional 1.5-times increased risk of dementia, but not MCI or CN-AR. LCA revealed four distinctive sub-populations: 1) frontal/low comorbidity; 2) high prevalence/high comorbidity; 3) affective/low comorbidity; and 4) sleep/low comorbidity. CONCLUSION Our findings confirm previous reports on the prevalence of NPS in community-based samples and are consistent with the profiles of NPS domain characteristics of MCI and dementia. Number of co-morbid NPS and not symptom clusters are associated with increased risk of dementia. Understanding such patterns will help inform our understanding of mild behavioral disorders and assist with clinical assessment.
Abnormal White Matter Integrity in the Corpus Callosum among Smokers: Tract-Based Spatial Statistics

In the present study, we aimed to investigate the difference in white matter between smokers and nonsmokers. In addition, we examined relationships between white matter integrity and nicotine dependence parameters in smoking subjects. Nineteen male smokers were enrolled in this study. Eighteen age-matched non-smokers with no current or past psychiatric history were included as controls. Diffusion tensor imaging scans were performed, and the analysis was conducted using a tract-based special statistics approach. Compared with nonsmokers, smokers exhibited a significant decrease in fractional anisotropy (FA) throughout the whole corpus callosum. There were no significant differences in radial diffusivity or axial diffusivity between the two groups. There was a significant negative correlation between FA in the whole corpus callosum and the amount of tobacco use (cigarettes/day; R = − 0.580, p = 0.023). These results suggest that the corpus callosum may be one of the key areas influenced by chronic smoking.
Serum Thymidine Kinase 1, Canine‐C‐Reactive Protein, Haptoglobin, and Vitamin D Concentrations in Dogs with Immune‐Mediated Hemolytic Anemia, Thrombocytopenia, and Polyarthropathy

Background Relapses of immune‐mediated hemolytic anemia (IMHA), thrombocytopenia (ITP), or polyarthropathy (IMPA) occur despite normal hematologic and cytologic parameters. Thymidine kinase 1 (TK1), canine C‐reactive protein (c‐CRP), haptoglobin (HPT), and 25‐Hydroxyvitamin‐D (25(OH)D) might be adjunct to current monitoring strategies. Hypothesis/Objectives Compare serum concentrations of TK1, c‐CRP, HPT, and 25(OH)D in dogs with well‐ and poorly controlled primary IMHA, ITP, or IMPA. Animals Thirty‐eight client‐owned dogs. Methods Prospective descriptive study. Dogs diagnosed with IMHA, ITP, or IMPA had serum biomarker concentrations measured commercially. Disease control was assessed by hematocrit/PCV and reticulocyte count, platelet count, and synovial fluid cytology for IMHA, ITP, and IMPA, respectively. Statistical analysis performed by Mann‐Whitney rank‐sum tests and receiver operating characteristic curves. Results TK1 and c‐CRP, but not HPT significantly decreased with well‐ versus poorly controlled IMHA (P = 0.047, P = 0.028, P = 0.37). C‐CRP, but not TK or HPT was significantly lower with well‐ versus poorly controlled IMPA (P = 0.05, P = 0.28, P = 0.84). Sensitivity and specificity of TK and c‐CRP (simultaneously) for detecting dogs with poorly controlled IMHA were 88 and 100%, respectively. Sensitivity and specificity of c‐CRP for detecting poorly controlled dogs with IMPA were 13 and 100%, respectively. 92% of dogs were vitamin D insufficient (<100 ng/mL) regardless of disease control. Conclusions and Clinical Importance Combining TK1 and c‐CRP might act markers of disease control in dogs with IMHA. Canine‐CRP cannot be recommended as an independent marker of disease control in IMPA. 25(OH)D insufficiency in immune‐mediated disorders might benefit from further study to determine if supplementation could improve therapeutic response or reduce disease risk.
Gene transcription in sea otters (Enhydra lutris); development of a diagnostic tool for sea otter and ecosystem health

Gene transcription analysis for diagnosing or monitoring wildlife health requires the ability to distinguish pathophysiological change from natural variation. Herein, we describe methodology for the development of quantitative real‐time polymerase chain reaction (qPCR) assays to measure differential transcript levels of multiple immune function genes in the sea otter (Enhydra lutris); sea otter‐specific qPCR primer sequences for the genes of interest are defined. We establish a ‘reference’ range of transcripts for each gene in a group of clinically healthy captive and free‐ranging sea otters. The 10 genes of interest represent multiple physiological systems that play a role in immuno‐modulation, inflammation, cell protection, tumour suppression, cellular stress response, xenobiotic metabolizing enzymes, antioxidant enzymes and cell–cell adhesion. The cycle threshold (CT) measures for most genes were normally distributed; the complement cytolysis inhibitor was the exception. The relative enumeration of multiple gene transcripts in simple peripheral blood samples expands the diagnostic capability currently available to assess the health of sea otters in situ and provides a better understanding of the state of their environment.
Loss of TLR4 in mouse Müller cells inhibits both MyD88-dependent and –independent signaling

Müller cells are key to metabolic and ionic regulation in the retina. They also produce a number of inflammatory mediators and are significantly affected in diabetic retinopathy. To investigate the role of toll-like receptor 4 (TLR4) in retinal Müller cells, we crossed TLR4 floxed with PDGFRα-Cre mice to eliminate TLR4 in retinal Müller cells. We performed Western blotting and ELISA analyses to determine whether loss of TLR4 affected myeloid differentiation primary response protein (MyD88)-dependent or –independent signaling, leading to reduced levels of tumor necrosis factor alpha (TNFα) and interleukin 1 beta (IL1β) in whole retinal lysates from the TLR4 floxed and TLR4-PDGFRα-Cre mice. Data show that TLR4-PDGFRα-Cre mice have reduced levels of both the MyD88-dependent and -independent signaling pathways. These studies confirm successful development of a Müller cell-specific TLR4 knockout mouse colony. These mice have reduced MyD88-dependent and –independent signaling pathway proteins, as well as reduced TNFα and IL1β levels. These mice can be used to dissect TLR4 signaling in disorders affecting retinal Müller cells.
Delta Opioid Receptors Regulate Temporoammonic-Activated Feedforward Inhibition to the Mouse CA1 Hippocampus

The opioid system influences learning and memory processes. However, neural mechanisms underlying the modulation of hippocampal activity by opioid receptors remain largely unknown. Here, we compared how mu and delta receptors operate within the mouse CA1 network, and used knock-in mice expressing functional delta opioid receptors fused to the green fluorescent protein (DOR-eGFP) to determine how delta opioid receptor-expressing interneurons integrate within the hippocampal circuitry. Through whole cell patch-clamp recording of CA1 pyramidal neurons from wild-type and DOR-eGFP mice, we found that mu and delta receptors both modulate spontaneous GABAergic inhibition received by these cells. Interestingly, mu but not delta receptor activation decreased the feed-forward inhibitory input evoked by Schaffer collateral stimulation. However, mu and delta agonists modulated GABAergic feed-forward inhibition when evoked upon stimulation of the temporoammonic pathway. In addition, anterograde tracing using biotinylated dextran amine injected into the entorhinal cortex of DOR-eGFP mice suggests the existence of synaptic contacts between temporoammonic afferents and delta receptor-expressing interneurons processes in CA1. Altogether, our data demonstrate a distinct modulatory role of the hippocampal network activity by mu and delta opioid receptors, and show for the first time that delta receptor-expressing interneurons in the CA1 are recruited by the temporoammonic pathway rather than the Schaffer collateral.
Association Between Employment Status and Objectively Measured Physical Activity and Sedentary Behavior—The Maastricht Study

Objective: To examine the association between employment status and physical activity and sedentary behavior. Methods: We included 2045 participants from The Maastricht Study, who used a thigh-worn accelerometer. We compared time spent sedentary, standing, stepping, and higher intensity physical activity between participants with different employment status (non-employed or low-, intermediate- or high-level occupation) with analysis of variance. Results: Participants in low-level occupations were less sedentary and standing and stepping more than those in other occupational categories and non-employed participants. Among the employed, the differences were mostly observed on weekdays, whereas the differences in sedentary time and standing between those in low-level occupations and non-employed participants were evident both on weekdays and weekend days. Conclusions: Those in low-level occupational category were less sedentary and more active than non-employed and those in other occupational categories, especially on weekdays.
Translational Epidemiology and the Application of Public Health Surveillance : Diabetes Mellitus and Mental Distress in New York City before and After the September 11 , 2001 Attacks

Objective: We aimed to test the hypothesis that there were significant increases in the prevalence of diabetes mellitus (DM) and mental distress from 1999 to 2009 in the state of New York (NY), and that these increases may be partly attributable to the catastrophic event of the September 11, 2001 attacks in central NY City (NYC) as compared to the other counties in the state of NY (RNY). Study Design: A cross-sectional analysis. Methods: Data (n=60,286) from 1999-2009 Behavioral Risk Factor Surveillance System in the state of NY were used to examine age-adjusted prevalence of DM in NYC as compared to RNY for three time periods: 1 (1999-2000), 2 (2001-2002, represents the year of the attacks), and 3 (2009). Associations of DM with mental distress and other risk factors were examined cross-sectionally using multiple logistic regression analysis. Results: Residents living in NYC had a significantly higher prevalence of DM and mental distress than those living in RNY (p<0.001). Age-adjusted prevalence of DM was 7.1% vs. 5.3% in period 1, 8.0% vs. 6.2% in period 2, and 10.3% vs. 7.5% in period 3 for NYC versus RNY, respectively. The corresponding values of the prevalence of mental distress were 13.0% vs. 11.1%, 14.3% vs. 11.9%, and 16.6% vs. 12.4%, for study periods 1 to 3 respectively. Using the combined data (1999-2009), multivariate logistic regression analysis indicate that the prevalence of DM was significantly associated with mental distress, being overweight, obesity, smoking and lower socioeconomic status (SES). Conclusion: The prevalence of DM and mental distress significantly increased from 1999 to 2009 in NYC and RNY. Residents who lived in NYC had significantly higher prevalence of DM and mental distress than those living in RNY. Subjects with DM were significantly associated with mental distress, abnormal body weight, smoking and lower SES. The significantly increased trend in DM and its risk factors including mental distress from 2001-2002 to 2009 may be partially explained by a possible middle and long-term impact of the September 11, 2001 attacks.
Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice

Lentinula edodes-derived polysaccharides possess many therapeutic characteristics, including anti-tumor and immuno-modulation. The gut microbes play a critical role in modulation of immune function. However, the impact of Lentinula edodes-derived polysaccharides on the gut microbes have not yet been explored. In this study, high-throughput pyrosequencing technique was employed to investigate the effects of a new heteropolysaccharide L2 from Lentinula edodes on microbiota diversity and composition of small intestine, cecum, colon and distal end of colon (feces) in mice. The results demonstrated that along mouse intestine the microbiota exhibit distinctly different space distribution. L2 treatment reduced the diversity and evenness of gut microbiota along the intestine, especially in the cecum and colon. In the fecal microbial communities, the decrease of Bacteroidetes by significantly increasing Proteobacteria were observed, which were characterized by the increased Helicobacteraceae and reduced S24-7 at family level. Some OTUs, corresponding to Bacteroides acidifaciens, Alistipes and Helicobacter suncus, were found to be significantly increased in L2 treated-mice. In particular, 4 phyla Chloroflexi, Gemmatimonadetes, Nitrospirae and Planctomycetes are exclusively present in L2-treated mice. This is helpful for further demonstrating healthy action mechanism of Lentinula edodes-derived polysaccharide L2.
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

Motivation: Recent transcriptome studies have revealed that total transcript numbers vary by cell type and condition; therefore, the statistical assumptions for single-cell transcriptome studies must be revisited. SAMstrt is an extension code for SAMseq, which is a statistical method for differential expression, to enable spike-in normalization and statistical testing based on the estimated absolute number of transcripts per cell for single-cell RNA-seq methods. Availability and Implementation: SAMstrt is implemented on R and available in github (https://github.com/shka/R-SAMstrt). Contact: shintaro.katayama@ki.se Supplementary Information: Supplementary data are available at Bioinformatics online.