Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of Basidiomycetes in Michigan Agricultural Soils

ABSTRACT We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With “species” defined as organisms yielding PCR products with ≥99% identity in the 5′ 650 bases of the nuclear large-subunit ribosomal DNA, 241 “species” were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 “species” had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple “species” could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated “species” richness for this 11.2-ha site was 367 “species” of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure.
Differential response to amphetamine in schizophrenia

Abstract Amphetamine added to maintenance therapy with neuroleptic drugs was accompanied by relief of complaints in 32 of 48 chronic schizophrenic patients with a long‐standing incapacity for work. In 22 cases this relief was followed by increased work efficiency. These gains were lost at experimental withdrawal of amphetamine. The response to amphetamine varied with type of schizophrenic symptomatology. All current regressive symptoms meant worsening in spite of concomitant neuroleptic treatment, in accordance with the dopamine hypothesis. Non‐regressive subjects displaying florid symptoms, however, benefited. Worsening, in a few cases, occurred only in the absence of neuroleptics. A few subjects with negative symptoms only, seemed totally unresponsive. These findings point at variations in sensitivity to dopaminergic stimulation in schizophrenic subjects. Worsening and improvement with amphetamine were each clearly connected with type of symptomatology only when current psycholic or florid non‐regressive symptoms were exhibited. In cases with negative symptoms only, the type of response could not be reliably based on clinical data. Studies of autonomic functioning and attention were therefore performed in a sub‐sample. Skin conductance level, reactivity and habituation rate were found to be lower in positive responders before amphetamine. After amphetamine there were no such differences. Attention tests showed no initial differences between groups but the performance of positive responders improved with amphetamine.
LDPC decoder implementation using FPGA

This paper presents a partial-parallel LDPC decoder based on sum-product algorithm with high throughput. The hardware implementation of decoder considers design issues with respect to FPGA and time scheduling is proposed based on modified TPMP1 algorithm in order to reduce the number of clock cycles, hardware resources and power. The decoder is implemented for a code length of 672 whit rate of 3/4, maximum throughput of 3360 Mbps in maximum frequency of 280 MHz and provides power of 150 mW.
Monte Carlo Investigation of Size-Dependent Impact Ionization Properties in InP Under Submicron Scale

The impact ionization properties in InP have been studied by using an ensemble Monte Carlo (EMC) method. In our EMC model, analytical model which contains three conduction bands and three valance bands is adopted to describe the band structure. The electron and hole impact ionization rate is fitted to the available measurement in the wide range of electric field by using Keldysh formula. The steady properties of InP are presented and analyzed. Particularly, the impact ionization behaviors in InP under submicron scale are discussed in detail. It is found that the impact ionization coefficient is not only a function of the applied electric filed but also behaves a size-dependent property when the size is down to submicron scale. We also find that, the size-dependent impact ionization effect which results from the dead space effect and the confined size, can help to prevent the carriers from impact ionization. Finally, the ratio of the electron impact ionization coefficient and the hole impact ionization coefficient is further studied. By taking the size-dependent impact ionization effect into consideration, this ratio is no longer holding as a constant but changing with the size of the devices under the specific electric field. As the size scaling down, the ratio will tend to deviate from one unit, which may contribute to a new look at the noise theory of APD devices.
Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells

Hepatocytes generated from human induced pluripotent stem cells (hiPSCs) are unprecedented resources for pharmaceuticals and cell therapy. However, the in vitro directed differentiation of human pluripotent stem cells into mature hepatocytes remains challenging. Little attention has so far been paid to variations among hiPSC lines in terms of their hepatic differentiation. In the current study, we developed an improved hepatic differentiation protocol and compared 28 hiPSC lines originated from various somatic cells and derived using retroviruses, Sendai viruses, or episomal plasmids. This comparison indicated that the origins, but not the derivation methods, may be a major determinant of variation in hepatic differentiation. The hiPSC clones derived from peripheral blood cells consistently showed good differentiation efficiency, whereas many hiPSC clones from adult dermal fibroblasts showed poor differentiation. However, when we compared hiPSCs from peripheral blood and dermal fibroblasts from the same individuals, we found that variations in hepatic differentiation were largely attributable to donor differences, rather than to the types of the original cells. These data underscore the importance of donor differences when comparing the differentiation propensities of hiPSC clones.
A finite element analysis of the effect of electrode area and inter-electrode distance on the spatial distribution of the current density in tDCS

We investigated the effect of electrode area and inter-electrode distance on the spatial distribution of the current density in transcranial direct current stimulation (tDCS). For this purpose, we used the finite element method to compute the distribution of the current density in a four-layered spherical head model using various electrode montages, corresponding to a range of electrode sizes and inter-electrode distances. We found that smaller electrodes required slightly less current to achieve a constant value of the current density at a reference point on the brain surface located directly under the electrode center. Under these conditions, smaller electrodes also produced a more focal current density distribution in the brain, i.e. the magnitude of the current density fell more rapidly with distance from the reference point. The combination of two electrodes with different areas produced an asymmetric current distribution that could lead to more effective and localized neural modulation under the smaller electrode than under the larger one. Focality improved rapidly with decreasing electrode size when the larger electrode sizes were considered but the improvement was less marked for the smaller electrode sizes. Also, focality was not affected significantly by inter-electrode distance unless two large electrodes were placed close together. Increasing the inter-electrode distance resulted in decreased shunting of the current through the scalp and the cerebrospinal fluid, and decreasing electrode area resulted in increased current density on the scalp under the edges of the electrode. Our calculations suggest that when working with conventional electrodes (25–35 cm2), one of the electrodes should be placed just ‘behind’ the target relative to the other electrode, for maximum current density on the target. Also electrodes with areas in the range 3.5–12 cm2 may provide a better compromise between focality and current density in the scalp than the traditional electrodes. Finally, the use of multiple small return electrodes may be more efficient than the use of a single large return electrode.
An integrated acceleration sensor for traffic condition detection

An acceleration sensor used to determine the vehicles speeds on the highways is developed. The sensor is able to measure the vibrational accelerations perpendicular (out-of-plane) to the asphalt surface as low as 1 mG. The sensor structure is validated with the engineering software packages: ANSYS, COVENTOR and Matlab.
A small‐sample multivariate kernel machine test for microbiome association studies

High‐throughput sequencing technologies have enabled large‐scale studies of the role of the human microbiome in health conditions and diseases. Microbial community level association test, as a critical step to establish the connection between overall microbiome composition and an outcome of interest, has now been routinely performed in many studies. However, current microbiome association tests all focus on a single outcome. It has become increasingly common for a microbiome study to collect multiple, possibly related, outcomes to maximize the power of discovery. As these outcomes may share common mechanisms, jointly analyzing these outcomes can amplify the association signal and improve statistical power to detect potential associations. We propose the multivariate microbiome regression‐based kernel association test (MMiRKAT) for testing association between multiple continuous outcomes and overall microbiome composition, where the kernel used in MMiRKAT is based on Bray‐Curtis or UniFrac distance. MMiRKAT directly regresses all outcomes on the microbiome profiles via a semiparametric kernel machine regression framework, which allows for covariate adjustment and evaluates the association via a variance‐component score test. Because most of the current microbiome studies have small sample sizes, a novel small‐sample correction procedure is implemented in MMiRKAT to correct for the conservativeness of the association test when the sample size is small or moderate. The proposed method is assessed via simulation studies and an application to a real data set examining the association between host gene expression and mucosal microbiome composition. We demonstrate that MMiRKAT is more powerful than large sample based multivariate kernel association test, while controlling the type I error. A free implementation of MMiRKAT in R language is available at http://research.fhcrc. org/wu/en.html.
Allele C‐specific methylation of the 5‐HT2A receptor gene: Evidence for correlation with its expression and expression of DNA methylase DNMT1

Differential DNA methylation has been suggested to contribute to differential activity of alleles C and T and thereby to genetic associations between the C/T(102) polymorphism in the 5‐HT2A receptor gene (5HT2AR) and psychiatric disorders. We surveyed methylation in two CpG sites, which are specific to allele C. The majority of allele C‐specific CpG sites were methylated in human temporal cortex and peripheral leukocytes and levels of methylation varied between individuals. Levels of methylation in the promoter correlated significantly with the expression of 5HT2AR. Methylation of allele C‐specific CpG sites in the first exon correlated significantly with the expression of DNA methylase 1 (DNMT1) but not S‐adenosylhomocysteine hydrolase (AHCY). These findings support the hypothesis that allele‐specific DNA methylation is involved in regulation of 5HT2AR expression, influencing expression differences between alleles C and T. © 2005 Wiley‐Liss, Inc.
Diagnosis of fibrosis and cirrhosis using liver stiffness measurement in nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is one of the most common liver diseases in affluent countries. Accurate noninvasive tests for liver injury are urgently needed. The aim of this study was to evaluate the accuracy of transient elastography for the diagnosis of fibrosis and cirrhosis in patients with NAFLD and to study factors associated with discordance between transient elastography and histology. Two hundred forty‐six consecutive patients from two ethnic groups had successful liver stiffness measurement and satisfactory liver biopsy specimens. The area under the receiver‐operating characteristics curve (AUROC) of transient elastography for F3 or higher and F4 disease was 0.93 and 0.95, respectively, and was significantly higher than that of the aspartate aminotransferase–to–alanine aminotransferase ratio, aspartate aminotransferase–to–platelet ratio index, FIB‐4, BARD, and NAFLD fibrosis scores (AUROC ranged from 0.62 to 0.81, P < 0.05 for all comparisons). At a cutoff value of 7.9 kPa, the sensitivity, specificity, and positive and negative predictive values for F3 or greater disease were 91%, 75%, 52%, and 97%, respectively. Liver stiffness was not affected by hepatic steatosis, necroinflammation, or body mass index. Discordance of at least two stages between transient elastography and histology was observed in 33 (13.4%) patients. By multivariate analysis, liver biopsy length less than 20 mm and F0‐2 disease were associated with discordance. Conclusion: Transient elastography is accurate in most NAFLD patients. Unsatisfactory liver biopsy specimens rather than transient elastography technique account for most cases of discordance. With high negative predictive value and modest positive predictive value, transient elastography is useful as a screening test to exclude advanced fibrosis. Liver biopsy may be considered in NAFLD patients with liver stiffness of at least 7.9 kPa. (HEPATOLOGY 2010;51:454–462.)
“Being Bipolar”: A Qualitative Analysis of the Experience of Bipolar Disorder as Described in Internet Blogs

ABSTRACT In the light of debates about the nature of bipolar disorder (BD), the current article presents a thematic analysis of Internet “blogs” by self-identified bipolar sufferers. Extreme and frequent fluctuation of mood was considered the principal feature of BD, along with a broad range of other problems. BD was often invoked as an explanation for life difficulties or lack of achievement, and was mostly regarded as a brain disease. Most bloggers emphasized the importance of drug treatment, along with the self-management techniques. The blogs present a “bipolar identity,” which is much broader than traditional definitions, are based on a medicalized model of the disorder, and are connected to the moral function of enabling people to externalize unwanted aspects of the self.
An American Sleep Disorders Association Review The Role of Actigraphy in the Evaluation of Sleep Disorders

Summary: This paper, which has been reviewed and approved by the Board of Directors of the American Sleep Disorders Association, provides the background for the Standards of Practice Committee's parameters for the practice of sleep medicine in North America. The growing use of activity-based monitoring (actigraphy) in sleep medicine and sleep research has enriched and challenged traditional sleep-monitoring techniques. This review summarizes the empirical data on the validity of actigraphy in assessing sleep-wake patterns and assessing clinical and control groups ranging in age from infancy to elderly. An overview of sleep-related actigraphic studies is also included. Actigraphy provides useful measures of sleep-wake schedule and sleep quality. The data also suggest that actigraphy, despite its limitations, may be a useful, cost-effective method for assessing specific sleep disorders, such as insomnia and schedule disorders, and for monitoring their treatment process. Methodological issues such as the proper use of actigraphy and possible artifacts have not been systematically addressed in clinical research and practice.
Expression of caspase activation recruitment and pyrin domain levels of apoptosis-associated speck-like protein complex in the pancreas of rats subjected to experimental pancreatitis

The present study investigated the effect of rutin, a natural flavonoid, on the expression of caspase activation recruitment domain (CARD) and pyrin domain (PYD) of apoptosis-associated speck-like protein (ASC), a mediator of inflammation, in the pancreas of rats administered with ethanol (EtOH) and high-fat diet (HFD). Pancreatitis was induced in male albino Wistar rats by administering EtOH (8–12 g/kg/day) and HFD (22% fat) for 90 days. In addition, rats also received 100 mg rutin/kg body weight orally from 31st day till the experimental period. Serum levels of cytokines, interleukin 18 (IL-18) and IL-6; activity levels of caspase-1 and myeloperoxidase (MPO); messenger RNA (mRNA) expression of tumor necrosis factor α (TNF-α), caspase-1, CARD and PYD of ASC; and histological changes in pancreas were assessed. We observed a significant elevation in serum IL-18, IL-6, caspase-1 and MPO activities, mRNA expression of PYD, TNF-α and caspase-1 in the pancreas of rats administered with EtOH and HFD. Rutin administration along with EtOH and HFD significantly upregulated the mRNA expression of CARD and downregulated PYD, caspase-1, and TNF-α expressions. Rutin supplementation was also found to reduce IL-18 and IL-6 levels; and inflammatory changes in tissue architecture were evidenced by histological observations. The anti-inflammatory activity of rutin might be due to its effect on modulating the expression of ASC complex that mediates inflammation.
Neural circulatory control during exercise: early insights

• What is the topic of this lecture? Sir William Paton, a distinguished physician scientist, was interested in the origins of concepts in physiology. This lecture explores the early insights on the neural control of the circulation during exercise. • What advances does it highlight? This lecture presents some of the outstanding seminal investigations on the central and peripheral control mechanisms that regulate the autonomic neural activity to the heart and blood vessels during exercise.
Indigenous evolution of Plasmodium falciparum pyrimethamine resistance multiple times in Africa

Objectives Resistance to pyrimethamine in Plasmodium falciparum is conferred by mutations in the gene encoding dihydrofolate reductase (DHFR). It is known that DHFR double mutants have evolved independently in multiple geographic areas, whereas the triple mutant prevalent in Africa appears to have originated in south-east Asia. In this study, we investigated whether other triple mutants may have evolved independently in Africa. Methods We determined the DHFR genotypes and haplotypes of five microsatellite loci flanking the DHFR locus between 4.49 kb upstream and 1.48 kb downstream of 159 isolates collected from three African countries (Republic of Congo, Ghana and Kenya). Results The CIRNI type of DHFR triple mutant (with mutations underlined at amino acid positions 51, 59 and 108) was predominant in the Republic of Congo (82%) and Ghana (81%) and was the second most prevalent in Kenya (27%), where the CICNI type of DHFR double mutant was dominant. Three distinct microsatellite haplotypes were identified in the DHFR triple mutant. One haplotype was identical to that originating in south-east Asia. The other two haplotypes occurred in Ghana and Kenya, which were unique, previously undescribed and identical to those of the two DHFR double mutants found in the same locations. Conclusions This study presents strong evidence for the unique, multiple independent evolution of pyrimethamine resistance in Africa. Indigenous evolution of the triple mutant from the double mutant appears to have occurred in a step-wise manner in Kenya and Ghana or in nearby countries in east and west Africa.
Thermoregulatory sweat testing in patients with erythromelalgia.

OBJECTIVES To examine the results of thermoregulatory sweat testing in patients with erythromelalgia and to compare them with the results of other neurophysiologic tests of small-fiber nerve function. DESIGN Retrospective study. SETTING Tertiary referral center. PATIENTS Thirty-two consecutive patients with erythromelalgia who had thermoregulatory sweat testing in addition to vascular and nerve testing. INTERVENTION The following information was abstracted for each patient: demographics, clinical presentation, and results of thermoregulatory sweat testing, vascular (noninvasive) testing, and nerve testing (electromyography and autonomic reflex screen, including quantitative sudomotor axon reflex test). MAIN OUTCOME MEASURES Results of thermoregulatory sweat testing to evaluate small-fiber neuropathy, compared with other tools used to estimate small-fiber neuropathy. RESULTS Thermoregulatory sweat testing results were abnormal in 28 (88%) of 32 patients, and quantitative sudomotor axon reflex test results were abnormal in 22 patients (69%). Abnormalities noted on thermoregulatory sweat testing varied from local hypohidrosis or anhidrosis to global anhidrosis. Global or almost-global anhidrosis was present in 8 patients (25%); in 19 patients (59%) the anhidrosis was distal, and 1 other patient (3%) had a less specific pattern of anhidrosis (multifocal or regional). The area of anhidrosis generally corresponded to the area that was symptomatic of the erythromelalgia. CONCLUSIONS Small-fiber neuropathy is prevalent in most patients with erythromelalgia. Thermoregulatory sweat testing is a sensitive and useful marker of small-fiber neuropathy in these patients.
Functional Interaction between the Scaffold Protein Kidins220/ARMS and Neuronal Voltage-Gated Na+ Channels*

Background: Tight regulation of ion channel activity is essential for neuronal function. Results: The scaffold protein Kidins220 associates with brain voltage-gated sodium channels and modulates their activity. Conclusion: Lack of Kidins220 in mice causes deregulated sodium channel function in inhibitory neurons, ultimately leading to impaired network excitability. Significance: Kidins220 may help maintain the balance between excitation and inhibition in neural networks. Kidins220 (kinase D-interacting substrate of 220 kDa)/ankyrin repeat-rich membrane spanning (ARMS) acts as a signaling platform at the plasma membrane and is implicated in a multitude of neuronal functions, including the control of neuronal activity. Here, we used the Kidins220−/− mouse model to study the effects of Kidins220 ablation on neuronal excitability. Multielectrode array recordings showed reduced evoked spiking activity in Kidins220−/− hippocampal networks, which was compatible with the increased excitability of GABAergic neurons determined by current-clamp recordings. Spike waveform analysis further indicated an increased sodium conductance in this neuronal subpopulation. Kidins220 association with brain voltage-gated sodium channels was shown by co-immunoprecipitation experiments and Na+ current recordings in transfected HEK293 cells, which revealed dramatic alterations of kinetics and voltage dependence. Finally, an in silico interneuronal model incorporating the Kidins220-induced Na+ current alterations reproduced the firing phenotype observed in Kidins220−/− neurons. These results identify Kidins220 as a novel modulator of Nav channel activity, broadening our understanding of the molecular mechanisms regulating network excitability.